Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012447.1 Corchorus olitorius cultivar O-4 contig12480, 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: 117458
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2137 original size:11 final size:12
Alignment explanation
Indices: 2121--2152 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2111 GAAGTTTGTG
2121 TTTGAAGACT-A
1 TTTGAAGACTAA
2132 TTTGAAGA-TAA
1 TTTGAAGACTAA
2143 TTTGAAGACT
1 TTTGAAGACT
2153 TGAAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:2157 original size:19 final size:18
Alignment explanation
Indices: 2133--2168 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2123 TGAAGACTAT
2133 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
2152 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
2169 ATCATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:2790 original size:18 final size:19
Alignment explanation
Indices: 2762--2798 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2752 CTCTTCTTCT
2762 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
2781 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
2799 GGCTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:5581 original size:22 final size:21
Alignment explanation
Indices: 5529--5582 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
5519 GCTTCTTGAA
5529 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
5550 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
5569 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
5583 CACGAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:6238 original size:54 final size:54
Alignment explanation
Indices: 6142--6350 Score: 206
Period size: 54 Copynumber: 3.8 Consensus size: 54
6132 AAGTTTCCTA
* * ** *
6142 AAGTAATCTGGTGCGGTCAATCAAGAAAGTTTCCAGTTGTTTAGGTTTATCTTC
1 AAGTGATCTGATGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATCTTC
* *
6196 AAGTGATC-CAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAATTAAGTTTATCTTC
1 AAGTGATCTGA-TGCGGTCAATCAAGAAAGTTTATAGTGG--T--TTAGGTTTATCTTC
* * * *
6254 AAGTGATCTGATGCTGTCAGTAAAGAAAGTTTCA-AGTGGTTTGGGTTTATCTTC
1 AAGTGATCTGATGCGGTCAATCAAGAAAGTTT-ATAGTGGTTTAGGTTTATCTTC
* * * * *
6308 AAGAGATTTGATGCGGTCCATCAAGAAAGTGTCTAGTGGTTTA
1 AAGTGATCTGATGCGGTCAATCAAGAAAGTTTATAGTGGTTTA
6351 AGCTATTTAG
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
54 77 0.62
56 2 0.02
58 44 0.35
59 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (54 bp):
AAGTGATCTGATGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATCTTC
Found at i:6280 original size:58 final size:58
Alignment explanation
Indices: 6152--6295 Score: 156
Period size: 58 Copynumber: 2.6 Consensus size: 58
6142 AAGTAATCTG
* * * *
6152 GTGCGGTCAATCAAGAAAGTTTCCAGT--TGT--TTAGGTTTATCTTCAAGTGATCCA
1 GTGCGGTCAATAAAGAAAGTTTCAAGTGGTTTAATTAAGTTTATCTTCAAGTGATCCA
* *
6206 GTGCGGTCAATCAAGAAAGTTT-ATAGTGGTTTAATTAAGTTTATCTTCAAGTGAT-CT
1 GTGCGGTCAATAAAGAAAGTTTCA-AGTGGTTTAATTAAGTTTATCTTCAAGTGATCCA
* *
6263 GATGCTGTCAGTAAAGAAAGTTTCAAGTGGTTT
1 G-TGCGGTCAATAAAGAAAGTTTCAAGTGGTTT
6296 GGGTTTATCT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
54 25 0.33
56 2 0.03
57 2 0.03
58 46 0.61
59 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (58 bp):
GTGCGGTCAATAAAGAAAGTTTCAAGTGGTTTAATTAAGTTTATCTTCAAGTGATCCA
Found at i:6449 original size:35 final size:35
Alignment explanation
Indices: 6390--6487 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 35
6380 TTCTTCAAGA
* * * *
6390 TATTCGGATTGGTTCCGTGGGATCTTTCCTCAACT
1 TATTCGGATTGATTCAGTGCGATCTTTCATCAACT
* * *
6425 TATTCAGATTGATTCGGTGCGATCTTTCATCAAGT
1 TATTCGGATTGATTCAGTGCGATCTTTCATCAACT
* *
6460 TATTCGGGTTGATTCAGTGTGATCTTTC
1 TATTCGGATTGATTCAGTGCGATCTTTC
6488 TTAAAACTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.42
Consensus pattern (35 bp):
TATTCGGATTGATTCAGTGCGATCTTTCATCAACT
Found at i:6573 original size:46 final size:49
Alignment explanation
Indices: 6520--6639 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 49
6510 TTTCTTGTTT
6520 TTTGATTCGGTGAATCAAGTTAATGCGGTGC-A-TTATTTCTTCAAA-A
1 TTTGATTCGGTGAATCAAGTTAATGCGGTGCAATTTATTTCTTCAAAGA
* *
6566 TTTGATTCGGTGAATCAATTTAGTGCGGTGCAGTATTTATTTCTTCAAAGA
1 TTTGATTCGGTGAATCAAGTTAATGCGGTGCA--ATTTATTTCTTCAAAGA
* *
6617 -ATAATTCGGTGAATCAAGTTAAT
1 TTTGATTCGGTGAATCAAGTTAAT
6640 TGAGAGCAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
46 29 0.46
49 1 0.02
50 32 0.51
51 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (49 bp):
TTTGATTCGGTGAATCAAGTTAATGCGGTGCAATTTATTTCTTCAAAGA
Found at i:6631 original size:96 final size:92
Alignment explanation
Indices: 6524--6719 Score: 227
Period size: 96 Copynumber: 2.1 Consensus size: 92
6514 TTGTTTTTTG
* * * *
6524 ATTCGGTGAATCAAGTTAA-TGCGGTGCATTATTTCTTCAAAATT-TGATTCGGTGAATC-AATT
1 ATTCGGTGAATCAAGTTAATTG-AGAGCAATATTTCTTC--AATTGTGATCCGGTGAATCAAATT
* * *
6586 TAGTGCGGTGCAGTATTTATTTCTTCAAAGAATA
63 AACT-CGATGCAGTA--T-TTTCTTCAAAGAATA
*
6620 ATTCGGTGAATCAAGTTAATTGAGAGCAATATTTCTTCATTTGTGATCCGGTGAATCAAATTAAC
1 ATTCGGTGAATCAAGTTAATTGAGAGCAATATTTCTTCAATTGTGATCCGGTGAATCAAATTAAC
*
6685 TCGATGCAGTATTTTCTTCAAAGAATG
66 TCGATGCAGTATTTTCTTCAAAGAATA
6712 ATTCGGTG
1 ATTCGGTG
6720 TGATGTCTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
92 22 0.25
93 1 0.01
94 3 0.03
95 22 0.25
96 38 0.43
97 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (92 bp):
ATTCGGTGAATCAAGTTAATTGAGAGCAATATTTCTTCAATTGTGATCCGGTGAATCAAATTAAC
TCGATGCAGTATTTTCTTCAAAGAATA
Found at i:13576 original size:128 final size:128
Alignment explanation
Indices: 13427--13664 Score: 327
Period size: 128 Copynumber: 1.9 Consensus size: 128
13417 AACTTTTTTA
** *
13427 TTTTATTTTTTTGAATTTTCACTATTTTTCTG-TGGAAGATAATAGTATAAAAACCCTAAATCTA
1 TTTTATTTTTTTGAATTTTCACTATTTTTC-GATAAAACATAATAGTATAAAAACCCTAAATCTA
*
13491 AAATTTCAAGTAAATCGCA-CAACTAAAGAATGCAGAACAAAAATCAGAAATCCACCCTGTGAAT
65 AAATTTCAAGTAAATCGAACCAA-TAAAGAATGCAGAACAAAAATCAGAAATCCACCCTGTGAAT
* * * * *
13555 TTTTTTTTTTTTGAATTTTCACTATTTTTCGATAAAACCTAGTAGTATAAGAACCCTAAATCTCA
1 TTTTATTTTTTTGAATTTTCACTATTTTTCGATAAAACATAATAGTATAAAAACCCTAAATCTAA
* * * *
13620 AATTTCAAGTCAATCTAACCAATAATGAATGTAGAACAAAAATCA
66 AATTTCAAGTAAATCGAACCAATAAAGAATGCAGAACAAAAATCA
13665 CAAAATTCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
127 1 0.01
128 91 0.96
129 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.35
Consensus pattern (128 bp):
TTTTATTTTTTTGAATTTTCACTATTTTTCGATAAAACATAATAGTATAAAAACCCTAAATCTAA
AATTTCAAGTAAATCGAACCAATAAAGAATGCAGAACAAAAATCAGAAATCCACCCTGTGAAT
Found at i:14269 original size:20 final size:20
Alignment explanation
Indices: 14219--14274 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
14209 TCCGCAGGTG
*
14219 ACCCGCCCCTAGGTGA-CCCT
1 ACCCGCCCCTGGGT-ACCCCT
*
14239 A-CCGGCCCTGGGTACCCCT
1 ACCCGCCCCTGGGTACCCCT
14258 ACCCGCCCCTGGGTACC
1 ACCCGCCCCTGGGTACC
14275 ATCAAAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.12, C:0.50, G:0.23, T:0.14
Consensus pattern (20 bp):
ACCCGCCCCTGGGTACCCCT
Found at i:15640 original size:28 final size:28
Alignment explanation
Indices: 15608--15749 Score: 84
Period size: 28 Copynumber: 5.4 Consensus size: 28
15598 AGTTTAGGTC
15608 TTTTCAAAGTGGGAAAGTTCCCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAG
**** ****
15636 TTTTCAAAGTTTTCAA-TTTAGGTC---
1 TTTTCAAAGTGGGAAAGTTCCCATCAAG
*
15660 TTTTCAAAGTGGGAAGGTTCCCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAG
**** ***
15688 TTTTCAAAGTATTCAA-TTTAGATC---
1 TTTTCAAAGTGGGAAAGTTCCCATCAAG
15712 TTTTCAAAGTGGGAAAGTTCCCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAG
15740 TTTTCAAAGT
1 TTTTCAAAGT
15750 ATTCAATTTA
Statistics
Matches: 74, Mismatches: 32, Indels: 16
0.61 0.26 0.13
Matches are distributed among these distances:
24 23 0.31
25 9 0.12
27 9 0.12
28 33 0.45
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (28 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAG
Found at i:15640 original size:52 final size:52
Alignment explanation
Indices: 15556--15975 Score: 608
Period size: 52 Copynumber: 8.0 Consensus size: 52
15546 TTCATTCAAG
* *
15556 TTTTCAAAATGGGAAAGTTCCCATCATA-TTTTCAAAGTATTCAGTTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCA-AGTTTTCAAAGTATTCAATTTAGGTC
*
15608 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
* *
15660 TTTTCAAAGTGGGAAGGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGATC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
* *
15712 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGATA
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
* * *
15764 TTTTCAAAGCGGGAAAGTTCTCATCAGGTTTTCAAAGTATTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
* * * *
15816 TTTTCAAAGCGGGAAAGTTTCCATCAAGTTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
* *
15868 TTTTCAAAGTGGGAAAGTTCCCATCATCAAGTTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGGGAAAGTT-CC--CATCAAGTTTTCAAAGTATTCAATTTAGGTC
* *
15923 TTTTCAAAGTGGGAAAGTTCCCATCATCAAGTTTTCAAAGTGTTCGATTTAGG
1 TTTTCAAAGTGGGAAAGTT-CC--CATCAAGTTTTCAAAGTATTCAATTTAGG
15976 GAAAGGCCCC
Statistics
Matches: 342, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
51 1 0.00
52 258 0.75
53 1 0.00
55 82 0.24
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTC
Found at i:15903 original size:31 final size:31
Alignment explanation
Indices: 15868--15964 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 31
15858 AATTTAGCTC
15868 TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
*** * *
15899 TTTTCAAAGTGTTCAA-TT--TAGC-TC---
1 TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
15923 TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
15954 TTTTCAAAGTG
1 TTTTCAAAGTG
15965 TTCGATTTAG
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
24 13 0.27
25 2 0.04
27 4 0.08
28 4 0.08
30 2 0.04
31 24 0.49
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
TTTTCAAAGTGGGAAAGTTCCCATCATCAAG
Found at i:17760 original size:332 final size:332
Alignment explanation
Indices: 17149--17935 Score: 1450
Period size: 332 Copynumber: 2.4 Consensus size: 332
17139 TTATAAGTTT
*
17149 TAATGCAAACAAGAGATGACAAGGTAATAGGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
1 TAATGCAAACAAGAGATGACAAGGTAACAGGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
17214 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATATGTTTACT
66 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATATGTTTACT
* *
17279 GCATTATAATGTTCCATACCTAACAACTGCTTACTATCTTTACAAATATTAACAAGTTGAGCTAG
131 GCATTATAATGTTCAATACCTAACAACTGCTTACTATCTTTACAAATATTAACAAGTTGAGCCAG
* *
17344 AACACTTGAAGAGATATTGGAGATTTGGGAAGCAAAGATGGAAGCTGTTGATTGAGAGAATCATG
196 AACACTAGAAGAGAGATTGGAGATTTGGGAAGCAAAGATGGAAGCTGTTGATTGAGAGAATCATG
17409 TGATTGCTGAAGCTTTTATATTTTGCATAATTTATGTTTTTCGAAGAATTATTTTACATATAATT
261 TGATTGCTGAAGCTTTTATATTTTGCATAATTTATGTTTTTCGAAGAATTATTTTACATATAATT
17474 TATGTTA
326 TATGTTA
* *
17481 TAATGCAAACAAGAGATGACAAGGTAACAGGTGATTTGCTTTTGTTCATAGTGTTAATGAAGAAC
1 TAATGCAAACAAGAGATGACAAGGTAACAGGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
17546 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATATGTTTACT
66 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATATGTTTACT
*
17611 GCATTATAATGTTCAATACCTAACAACTGCTTACTATCTTTACAAATATTAACAGGTTGAGCCAG
131 GCATTATAATGTTCAATACCTAACAACTGCTTACTATCTTTACAAATATTAACAAGTTGAGCCAG
*
17676 AACA-TCAGAAGAGAGATTGGAGATTTGGGAAGCAAAGATGGAAGCTGTTGATTGAGAGAATTAT
196 AACACT-AGAAGAGAGATTGGAGATTTGGGAAGCAAAGATGGAAGCTGTTGATTGAGAGAATCAT
* *
17740 GTGATTGCTGAAGTTTTTATATTTTGCATAATTTATGTTTTTTGAAGAATTATTTTACATATAAT
260 GTGATTGCTGAAGCTTTTATATTTTGCATAATTTATGTTTTTCGAAGAATTATTTTACATATAAT
17805 TTATGTTA
325 TTATGTTA
*
17813 TAATGCAAACAAGAGATGACAAGGTAACATGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
1 TAATGCAAACAAGAGATGACAAGGTAACAGGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
17878 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATAT
66 TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATAT
17936 AATTATAATG
Statistics
Matches: 440, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
331 1 0.00
332 439 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (332 bp):
TAATGCAAACAAGAGATGACAAGGTAACAGGTGATTTGCTTTTATTCATAATGTTAATGAAGAAC
TTAGCTTAAGTTCTTCATATATGGTATTGAAAGGTACATAACTGTGAAAATTTGATATGTTTACT
GCATTATAATGTTCAATACCTAACAACTGCTTACTATCTTTACAAATATTAACAAGTTGAGCCAG
AACACTAGAAGAGAGATTGGAGATTTGGGAAGCAAAGATGGAAGCTGTTGATTGAGAGAATCATG
TGATTGCTGAAGCTTTTATATTTTGCATAATTTATGTTTTTCGAAGAATTATTTTACATATAATT
TATGTTA
Found at i:18017 original size:31 final size:30
Alignment explanation
Indices: 17982--18054 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
17972 ATACTCCACA
*
17982 GGTCCCTCTACTTACACAAAAGAATCAATTT
1 GGTCCCTCTACTTACA-AAAACAATCAATTT
**
18013 GGTCCCTCTAC-TACAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAACAATCAATTT
*
18042 AGTCCCTCTACTT
1 GGTCCCTCTACTT
18055 GCAACTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.57
30 5 0.14
31 11 0.30
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAACAATCAATTT
Found at i:18647 original size:16 final size:16
Alignment explanation
Indices: 18623--18653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18613 CTCTTCCTTT
*
18623 TACTGAATATATATAG
1 TACTAAATATATATAG
18639 TACTAAATATATATA
1 TACTAAATATATATA
18654 CTATTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TACTAAATATATATAG
Found at i:19309 original size:31 final size:30
Alignment explanation
Indices: 19239--19311 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
19229 ACAAAGTAGC
* *
19239 AAGTAGAGAGACTAAATTGACAATTTTTGT
1 AAGTAGAGGGACCAAATTGACAATTTTTGT
***
19269 AA-TAGAGGGACCAAATTGATTCTTTTGTGT
1 AAGTAGAGGGACCAAATTGACAATTTT-TGT
19299 AAGTAGAGGGACC
1 AAGTAGAGGGACC
19312 TGTGGGGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.53
30 7 0.19
31 10 0.28
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (30 bp):
AAGTAGAGGGACCAAATTGACAATTTTTGT
Found at i:19723 original size:17 final size:17
Alignment explanation
Indices: 19701--19734 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19691 TTTACTCTTT
19701 GTAGTCTTCAGTGTCTC
1 GTAGTCTTCAGTGTCTC
19718 GTAGTCTTCAGTGTCTC
1 GTAGTCTTCAGTGTCTC
19735 TCGCGCGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (17 bp):
GTAGTCTTCAGTGTCTC
Found at i:27723 original size:38 final size:38
Alignment explanation
Indices: 27672--27748 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
27662 ATCTTTATTT
27672 TTATCTTTATCTTTATATTACTAGTCATTACTTTCATG
1 TTATCTTTATCTTTATATTACTAGTCATTACTTTCATG
27710 TTATCTTTATCTTTATATTACTAGTCATTACTTTCATG
1 TTATCTTTATCTTTATATTACTAGTCATTACTTTCATG
27748 T
1 T
27749 GCGTTGCACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (38 bp):
TTATCTTTATCTTTATATTACTAGTCATTACTTTCATG
Found at i:28685 original size:14 final size:14
Alignment explanation
Indices: 28641--28687 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
28631 TGAAAAATAG
28641 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
28655 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
28668 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
28682 TAAAAT
1 TAAAAT
28688 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:28846 original size:149 final size:149
Alignment explanation
Indices: 28503--28900 Score: 667
Period size: 149 Copynumber: 2.7 Consensus size: 149
28493 GGTCAATCAC
*
28503 AATAACCTTTTAAATTAAAATGGTAAAAATAAAATAATTAT-AAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
* * * *
28567 AAAATAAAAATTTTAGTAGAATCAAACTATATATTATAAAATTTTAATATATCCAAGTTTTTAAT
66 AAAATAGAATTTTTAGTAGAATCAAACTATATATTAAAAAACTTTAATATATCCAAGTTTTTAAT
28632 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAA--GTAAA
28653 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
28718 AAAATAGATTTTTTAGTAGAATCAAACTATATATTAAAAAAACTTT-ATATATCCAAGTTTTTAA
66 AAAATAGAATTTTTAGTAGAATCAAACTATATATT-AAAAAACTTTAATATATCCAAGTTTTTAA
28782 TGAAAAATAGTAATAA-TAAA
130 TGAAAAATAGTAA-AAGTAAA
28802 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
* *
28867 AAAATAGAGTTTTTAGTATAATCAAACTATATAT
66 AAAATAGAATTTTTAGTAGAATCAAACTATATAT
28901 CTGGCCAAAC
Statistics
Matches: 237, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
149 101 0.43
150 40 0.17
151 86 0.36
152 10 0.04
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (149 bp):
AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
AAAATAGAATTTTTAGTAGAATCAAACTATATATTAAAAAACTTTAATATATCCAAGTTTTTAAT
GAAAAATAGTAAAAGTAAA
Found at i:37303 original size:16 final size:15
Alignment explanation
Indices: 37265--37306 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
37255 ACAGAGGTTG
37265 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
37280 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
37295 ACTAGAAAACAA
1 AC-AGAAAACAA
37307 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:43336 original size:16 final size:15
Alignment explanation
Indices: 43298--43336 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
43288 ACAGAGGTTG
43298 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
43313 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
43328 ACTAGAAAA
1 AC-AGAAAA
43337 TAAAGCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:44136 original size:20 final size:18
Alignment explanation
Indices: 44097--44132 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
44087 CTAGACCTAA
*
44097 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
44115 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
44133 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:46318 original size:18 final size:18
Alignment explanation
Indices: 46240--46318 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
46230 CCAACCTGTT
*
46240 AACACAATCCCAGCACCG
1 AACACAGTCCCAGCACCG
* *
46258 AACACAGTTCCAGCATCG
1 AACACAGTCCCAGCACCG
** * *
46276 AACATTGACCCAGCATCG
1 AACACAGTCCCAGCACCG
*
46294 AACACAGTCCCAACACCG
1 AACACAGTCCCAGCACCG
46312 AACACAG
1 AACACAG
46319 ATTCTGTTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.38, C:0.38, G:0.14, T:0.10
Consensus pattern (18 bp):
AACACAGTCCCAGCACCG
Found at i:50628 original size:16 final size:17
Alignment explanation
Indices: 50607--50639 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50597 ATAATACATG
50607 TTTGGGC-TTAATTTGT
1 TTTGGGCTTTAATTTGT
50623 TTTGGGCTTTAATTTGT
1 TTTGGGCTTTAATTTGT
50640 ATGCTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.58
Consensus pattern (17 bp):
TTTGGGCTTTAATTTGT
Found at i:51417 original size:41 final size:38
Alignment explanation
Indices: 51370--51873 Score: 176
Period size: 42 Copynumber: 12.8 Consensus size: 38
51360 AAAAAGAAGT
*
51370 TTTTTCAAAGTTTTCAATTCAGGGAAAGATCCCATTCAG
1 TTTTTC-AAGTTTTCAATTTAGGGAAAGATCCCATTCAG
* * *
51409 TAGTTTTCAACTTTTCAAATTTAGGGAAAAACCCCA-TCAG
1 T--TTTTCAAGTTTTC-AATTTAGGGAAAGATCCCATTCAG
* *
51449 TTTCTTCAAGATTTTTAATTTAGGGAAAGATCCCATTAAG
1 TTT-TTCAAG-TTTTCAATTTAGGGAAAGATCCCATTCAG
* * *
51489 -ATTTCAA------AA-TTACGGAAAGATCCCA-CCAAAG
1 TTTTTCAAGTTTTCAATTTAGGGAAAGATCCCATTC--AG
* * * *
51520 TATTTTTCAAAG-ATTCAAAATTATGGAAAGATCCCA-CCAAAG
1 --TTTTTC-AAGTTTTC-AATTTAGGGAAAGATCCCATTC--AG
* * * *
51562 TATTTTTCAAGTTTTCAAAATTAGGGGAAGAACCCA-CCAAAG
1 --TTTTTCAAGTTTTC-AATTTAGGGAAAGATCCCATTC--AG
* *
51604 TATTTTTCAAGTTTTCAAAATTAGGGAAAGATCCCA-CCAAAG
1 --TTTTTCAAGTTTTC-AATTTAGGGAAAGATCCCATTC--AG
* * *
51646 TATTTTTTCAAGGATTTCGAAATTAGGGAAAGATTCCA-TCAAG
1 ---TTTTTCAA-GTTTTC-AATTTAGGGAAAGATCCCATTC-AG
* *
51689 -CTTTCAAGATTTCTAA-TTAGGGAAAGATCCC-TTCAAG
1 TTTTTCAAGTTTTC-AATTTAGGGAAAGATCCCATTC-AG
* * *
51726 TTTGTTCAAGTCTTCCGATTTAGGGAAAGATCCCATCCAG
1 TTT-TTCAAGT-TTTCAATTTAGGGAAAGATCCCATTCAG
* * *
51766 TTTCTTTTTAAAGTTTTAAATTTAGGGAAAGATCCCATCCAG
1 ----TTTTTCAAGTTTTCAATTTAGGGAAAGATCCCATTCAG
*
51808 -TCTTCAAAG-TTT---TTTAGGGAAAGATCCCA-TCAAG
1 TTTTTC-AAGTTTTCAATTTAGGGAAAGATCCCATTC-AG
51842 TTTTTCAGAAGTTTT-AATTTAGGGAAAGATCC
1 TTTTTC--AAGTTTTCAATTTAGGGAAAGATCC
51874 TGTCATCCAG
Statistics
Matches: 382, Mismatches: 44, Indels: 78
0.76 0.09 0.15
Matches are distributed among these distances:
30 15 0.04
31 4 0.01
33 1 0.00
34 23 0.06
35 6 0.02
36 3 0.01
37 28 0.07
38 19 0.05
39 52 0.14
40 39 0.10
41 28 0.07
42 120 0.31
43 17 0.04
44 27 0.07
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (38 bp):
TTTTTCAAGTTTTCAATTTAGGGAAAGATCCCATTCAG
Found at i:51548 original size:42 final size:41
Alignment explanation
Indices: 51486--51719 Score: 262
Period size: 42 Copynumber: 5.6 Consensus size: 41
51476 AGATCCCATT
*
51486 AAGATTTCAAAATTACGGAAAGATCCCACCAAAGTATTTTTC
1 AAGA-TTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTC
*
51528 AAAGATTCAAAATTATGGAAAGATCCCACCAAAGTATTTTTC
1 -AAGATTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTC
* * *
51570 AAGTTTTCAAAATTAGGGGAAGAACCCACCAAAGTATTTTTC
1 AAG-ATTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTC
*
51612 AAGTTTTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTTC
1 AAG-ATTCAAAATTAGGGAAAGATCCCACCAAAGTA-TTTTTC
* * * *
51655 AAGGATTTCGAAATTAGGGAAAGATTCCATC-AAG---CTTTC
1 AA-GA-TTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTC
*
51694 AAGATTTC-TAATTAGGGAAAGATCCC
1 AAGA-TTCAAAATTAGGGAAAGATCCC
51720 TTCAAGTTTG
Statistics
Matches: 173, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 16 0.09
38 6 0.03
39 6 0.03
41 3 0.02
42 104 0.60
43 15 0.09
44 23 0.13
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (41 bp):
AAGATTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTC
Found at i:51632 original size:84 final size:86
Alignment explanation
Indices: 51488--51678 Score: 289
Period size: 84 Copynumber: 2.2 Consensus size: 86
51478 ATCCCATTAA
* * *
51488 GATTTCAAAATTACGGAAAGATCCCACCAAAGTATTTTTCAAAGATTCAAAATTATGGAAAGATC
1 GATTTCAAAATTAGGGAAAGAACCCACCAAAGTATTTTTCAAAGATTCAAAATTAGGGAAAGATC
51553 CCACCAAAGTA-TTTTTCAA-
66 CCACCAAAGTATTTTTTCAAG
* * *
51572 GTTTTCAAAATTAGGGGAAGAACCCACCAAAGTATTTTTC-AAGTTTTCAAAATTAGGGAAAGAT
1 GATTTCAAAATTAGGGAAAGAACCCACCAAAGTATTTTTCAAAG-ATTCAAAATTAGGGAAAGAT
51636 CCCACCAAAGTATTTTTTCAAG
65 CCCACCAAAGTATTTTTTCAAG
*
51658 GATTTCGAAATTAGGGAAAGA
1 GATTTCAAAATTAGGGAAAGA
51679 TTCCATCAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
83 3 0.03
84 66 0.69
85 8 0.08
86 18 0.19
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (86 bp):
GATTTCAAAATTAGGGAAAGAACCCACCAAAGTATTTTTCAAAGATTCAAAATTAGGGAAAGATC
CCACCAAAGTATTTTTTCAAG
Found at i:51709 original size:37 final size:39
Alignment explanation
Indices: 51651--51762 Score: 113
Period size: 37 Copynumber: 2.9 Consensus size: 39
51641 CAAAGTATTT
*
51651 TTTCAAGGATTTCGAAATTAGGGAAAGATTCCATCAAGC
1 TTTCAAGGATTTCGAAATTAGGGAAAGATCCCATCAAGC
* * *
51690 TTTCAA-GATTTC-TAATTAGGGAAAGATCCCTTCAAGTT
1 TTTCAAGGATTTCGAAATTAGGGAAAGATCCCATCAAG-C
** * *
51728 TGTTCAAGTCTTCCG-ATTTAGGGAAAGATCCCATC
1 T-TTCAAGGATTTCGAAATTAGGGAAAGATCCCATC
51763 CAGTTTCTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
37 21 0.35
38 7 0.12
39 11 0.18
40 21 0.35
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (39 bp):
TTTCAAGGATTTCGAAATTAGGGAAAGATCCCATCAAGC
Found at i:53638 original size:3 final size:3
Alignment explanation
Indices: 53589--53630 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
53579 CGCATGTTAA
*
53589 AAT AAT AAT AAT AAT AAT AAT ATT AA- AAT AAAT CAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AA
53631 GATAATAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56324 original size:15 final size:15
Alignment explanation
Indices: 56304--56335 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56294 CCTTGGGGGT
56304 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
56319 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
56334 TC
1 TC
56336 CACTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:57037 original size:66 final size:64
Alignment explanation
Indices: 56923--57047 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 64
56913 AGTAATTCTG
* *
56923 AACCTGATTTGAGTGTTGTTTAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
1 AACCTAATTTAAGTGTTGTTTAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
* * * *
56987 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTG-TT-TAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA
57048 AACAAATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 16 0.31
65 2 0.04
66 33 0.63
67 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (64 bp):
AACCTAATTTAAGTGTTGTTTAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
Found at i:57061 original size:33 final size:32
Alignment explanation
Indices: 56953--57095 Score: 126
Period size: 33 Copynumber: 4.3 Consensus size: 32
56943 TAATGACATG
* * *
56953 AAATCTGTTTTAGATGTTGTTAGTGATGATACC
1 AAATCTGTTTTAGGTGTTGTTTGTGATGA-AAC
* ** * *
56986 AAACCTAATTTAAGTGTTGTTTGTGATGACAC
1 AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
*
57018 TAAATTTGTTTTAGGTGTTGTTTGTGATGAAAC
1 -AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
* **
57051 AAATTCTGTTTT-GGATGCTAATTGTGATGAAAAC
1 AAA-TCTGTTTTAGG-TGTTGTTTGTGATG-AAAC
57085 AAATCTGTTTT
1 AAATCTGTTTT
57096 GGTTGATCAT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
32 6 0.07
33 75 0.85
34 7 0.08
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (32 bp):
AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
Found at i:63044 original size:54 final size:54
Alignment explanation
Indices: 62945--63047 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
62935 GATGGGGGTC
*
62945 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGAA
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAGAA
* *
62999 ACTTGAGTTGAAAACCCGCAAAGGGCGGCTCAAGCGGAA-GTTGGAAAAG
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAG-GGAAGGATGGAAAAG
63048 ACATAGTCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 42 0.93
55 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.33, T:0.14
Consensus pattern (54 bp):
ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAGAA
Found at i:64120 original size:84 final size:85
Alignment explanation
Indices: 63992--64152 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 85
63982 AAGAATGAGG
** * * * * * *
63992 CTGAAGACAGCTCACAGATGGATCTGAAGACAGTTCCTAAAAGATTTTGATATTGAGGCTGAAGA
1 CTGAAGACAGCTCACAGAAAGATCTGAAGACAGTTCCCAAAAGATTTTAAGATTAAGGCTAAACA
64057 CAGCTCACAGATAGATAGAT
66 CAGCTCACAGATAGATAGAT
* * *
64077 CTGAAGACAGCTC-CTGAAAGATTTGAAGACAGTTCCCGAAAGATTTTAAGATTAAGGCTAAACA
1 CTGAAGACAGCTCACAGAAAGATCTGAAGACAGTTCCCAAAAGATTTTAAGATTAAGGCTAAACA
64141 CAGCTCACAGAT
66 CAGCTCACAGAT
64153 CTGAAGACAT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 52 0.80
85 13 0.20
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (85 bp):
CTGAAGACAGCTCACAGAAAGATCTGAAGACAGTTCCCAAAAGATTTTAAGATTAAGGCTAAACA
CAGCTCACAGATAGATAGAT
Found at i:64121 original size:22 final size:22
Alignment explanation
Indices: 64073--64127 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
64063 ACAGATAGAT
* *
64073 AGATCTGAAGACAGCTCCTGAA
1 AGATTTGAAGACAGCTCCCGAA
*
64095 AGATTTGAAGACAGTTCCCGAA
1 AGATTTGAAGACAGCTCCCGAA
*
64117 AGATTTTAAGA
1 AGATTTGAAGA
64128 TTAAGGCTAA
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:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (22 bp):
AGATTTGAAGACAGCTCCCGAA
Found at i:66962 original size:16 final size:17
Alignment explanation
Indices: 66941--66973 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
66931 AATATACATG
66941 TTTGGGC-TTAATTTGT
1 TTTGGGCTTTAATTTGT
66957 TTTGGGCTTTAATTTGT
1 TTTGGGCTTTAATTTGT
66974 ATGCTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.58
Consensus pattern (17 bp):
TTTGGGCTTTAATTTGT
Found at i:67756 original size:40 final size:39
Alignment explanation
Indices: 67699--68197 Score: 216
Period size: 42 Copynumber: 12.9 Consensus size: 39
67689 ATCAAAAAGA
* * *
67699 AGTTTTTTCAAAGTTTTCAATTCAGGGAAAGATCCCATCC
1 AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCAT-C
*
67739 AGTAGTT-TTC-AGGTTTTCAAATTTAGGGAAAAATCCCATC
1 AGT--TTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATC
* *
67779 AGTTTCTTCAAGATTTTTAATTTAGGGAAAGAT-CC--C
1 AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCATC
* * *
67815 A-----TT-AA-GATTTCAAAATTAGGGAAAGATCCCACC
1 AGTTTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATC
* * *
67848 AAAGTATTTTTCAA-GTTTTCAAAATTAGGGAAAGATCCCACC
1 --AGT-TTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATC
* * * *
67890 AAAGTATTTTTTCAAGGATTTCGAAATTAGGGAAAGATTCCATC
1 --AG--TTTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATC
* * *
67934 AAG-CT-TTCAA-GATTTCTAA-TTAGGGAAATATCCCATC
1 -AGTTTCTTCAAGGTTTTC-AATTTAGGGAAAGATCCCATC
* * *
67971 AAGTTTATTCAA-GTCTTCCGATTTAGGGAAAGATCCCATCC
1 -AGTTTCTTCAAGGT-TTTCAATTTAGGGAAAGATCCCAT-C
* * *
68012 AGTTTCTTTTAAAGTTTTAAATTTAGGGAAAGATCCCATC
1 AGTTTC-TTCAAGGTTTTCAATTTAGGGAAAGATCCCATC
* *
68052 TAG--TCTTCAAAG-TTT---TTTAGGGAAATATCCCATCC
1 -AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCAT-C
* * * * *
68087 CGTTTCTTTTTAAAGTTTTAAATTTAGGGGAAGATCCCATCC
1 AGTTTC--TTCAAGGTTTTCAATTTAGGGAAAGATCCCAT-C
*
68129 AG--TCTTCAAAG-TTT---TTTAGGGAAAGATCCCATC
1 AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCATC
* *
68162 AAATTT-TTCAGAAGTTTT-AATTTAGGGAAAGATCCC
1 -AGTTTCTTCA-AGGTTTTCAATTTAGGGAAAGATCCC
68198 GTCATCCAGT
Statistics
Matches: 375, Mismatches: 39, Indels: 91
0.74 0.08 0.18
Matches are distributed among these distances:
29 3 0.01
30 16 0.04
31 4 0.01
33 2 0.01
34 36 0.10
35 6 0.02
36 8 0.02
37 28 0.07
38 31 0.08
39 50 0.13
40 48 0.13
41 51 0.14
42 56 0.15
43 11 0.03
44 25 0.07
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (39 bp):
AGTTTCTTCAAGGTTTTCAATTTAGGGAAAGATCCCATC
Found at i:67887 original size:72 final size:69
Alignment explanation
Indices: 67753--67887 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 69
67743 GTTTTCAGGT
* * * *
67753 TTTCAAATTTAGGGAAAAATCCCATCAGTTTCTTCAAGATTTTTAATTTAGGGAAAGATCCCATT
1 TTTCAAAATTAGGGAAAAATCCCACCAGTTTCTTCAAGATTTTAAAATTAGGGAAAGATCCCATT
67818 AAGA
66 AAGA
* *
67822 TTTCAAAATTAGGGAAAGATCCCACCAAAGTATTTTTCAAG-TTTTCAAAATTAGGGAAAGATCC
1 TTTCAAAATTAGGGAAAAATCCCACC--AGT-TTCTTCAAGATTTT-AAAATTAGGGAAAGATCC
67886 CA
62 CA
67888 CCAAAGTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
69 23 0.41
71 7 0.12
72 26 0.46
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (69 bp):
TTTCAAAATTAGGGAAAAATCCCACCAGTTTCTTCAAGATTTTAAAATTAGGGAAAGATCCCATT
AAGA
Found at i:68122 original size:76 final size:75
Alignment explanation
Indices: 67992--68197 Score: 310
Period size: 76 Copynumber: 2.8 Consensus size: 75
67982 AGTCTTCCGA
*
67992 TTTAGGGAAAGATCCCATCCAGTTTCTTTTAAAGTTTTAAATTTAGGGAAAGATCCCATCTAGTC
1 TTTAGGGAAAGATCCCATCCAGTTTCTTTTAAAGTTTTAAATTTAGGGAAAGATCCCATCCAGTC
68057 TTCAAAGTTT
66 TTCAAAGTTT
* * *
68067 TTTAGGGAAATATCCCATCCCGTTTCTTTTTAAAGTTTTAAATTTAGGGGAAGATCCCATCCAGT
1 TTTAGGGAAAGATCCCATCCAGTTTC-TTTTAAAGTTTTAAATTTAGGGAAAGATCCCATCCAGT
68132 CTTCAAAGTTT
65 CTTCAAAGTTT
** *
68143 TTTAGGGAAAGATCCCAT-CAAATT-TTTCAGAAGTTTT-AATTTAGGGAAAGATCCC
1 TTTAGGGAAAGATCCCATCCAGTTTCTTTTA-AAGTTTTAAATTTAGGGAAAGATCCC
68198 GTCATCCAGT
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
73 21 0.18
74 7 0.06
75 27 0.23
76 64 0.54
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (75 bp):
TTTAGGGAAAGATCCCATCCAGTTTCTTTTAAAGTTTTAAATTTAGGGAAAGATCCCATCCAGTC
TTCAAAGTTT
Found at i:70449 original size:21 final size:21
Alignment explanation
Indices: 70423--70493 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
70413 CCTTTTTTGG
*
70423 CCTTATAAAGTTTTTTAGTCA
1 CCTTATAAAGTTTTTTAGTAA
*
70444 CCTTATAAAGTGTTTTTACCTAA
1 CCTTATAAAGT-TTTTTA-GTAA
* *
70467 CCTTATTAAGATTTTTAGTAA
1 CCTTATAAAGTTTTTTAGTAA
*
70488 TCTTAT
1 CCTTAT
70494 TGTAGATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 19 0.45
22 12 0.29
23 11 0.26
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (21 bp):
CCTTATAAAGTTTTTTAGTAA
Found at i:71016 original size:82 final size:86
Alignment explanation
Indices: 70867--71046 Score: 287
Period size: 82 Copynumber: 2.1 Consensus size: 86
70857 AAAAACCTTG
* *
70867 TAAATTTTCTTGGTAAGCTTATAAATTTTTCATTAAACTTGAAAGCTTTTTAAATAGTTTTCTTA
1 TAAAATTT-TTGGTAAGCTTATAAA-TTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTA
70932 AATTTAT-T-CAATCACCTCGTT
64 AATTTATATCCAATCACCTCGTT
*
70953 TAAGATTTTTGGTAAGCTTATAAA-TTTC-TTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAA
1 TAAAATTTTTGGTAAGCTTATAAATTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAA
71016 TTTATATCCAATCACCTCGTT
66 TTTATATCCAATCACCTCGTT
71037 TAAAATTTTT
1 TAAAATTTTT
71047 AGTGATCTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
82 39 0.44
83 5 0.06
84 22 0.25
85 16 0.18
86 6 0.07
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (86 bp):
TAAAATTTTTGGTAAGCTTATAAATTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAA
TTTATATCCAATCACCTCGTT
Found at i:71838 original size:21 final size:21
Alignment explanation
Indices: 71796--71839 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
71786 TTAGTAAGCA
* *
71796 TTTTAGTAACTTTATTAAGTT
1 TTTTAGTAACCTTATGAAGTT
*
71817 TTTTAGTAACCTTA-GAAGGT
1 TTTTAGTAACCTTATGAAGTT
71837 TTT
1 TTT
71840 ATATACTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTAGTAACCTTATGAAGTT
Found at i:73761 original size:22 final size:22
Alignment explanation
Indices: 73731--73785 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
73721 TTGAAGTCAC
73731 AAATCGTGTTATTATTTACCGA
1 AAATCGTGTTATTATTTACCGA
*
73753 AAATTGTGTTATTATTTACCGA
1 AAATCGTGTTATTATTTACCGA
*
73775 AAATCATGTTA
1 AAATCGTGTTA
73786 CCGTGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
AAATCGTGTTATTATTTACCGA
Found at i:78898 original size:35 final size:35
Alignment explanation
Indices: 78799--78898 Score: 146
Period size: 35 Copynumber: 2.9 Consensus size: 35
78789 TTGCTTGATT
** *
78799 CTTAATTACACCGAATTAAGTTGACCATCAAATTC
1 CTTAATTACACCGAATTAAGTTGAATACCAAATTC
*
78834 CTTAATTACACCGAATTAAGTTGATTACCAAATTC
1 CTTAATTACACCGAATTAAGTTGAATACCAAATTC
* *
78869 CTTAATTATACCGAATCAAGTTGAATACCA
1 CTTAATTACACCGAATTAAGTTGAATACCA
78899 TTTCCTCAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (35 bp):
CTTAATTACACCGAATTAAGTTGAATACCAAATTC
Found at i:79580 original size:26 final size:26
Alignment explanation
Indices: 79551--79603 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
79541 CAAATTTATG
79551 CCTAAA-ACTAGAGGCCCAA-TATTAAC
1 CCTAAAGACTA-AGGCCCAACTA-TAAC
*
79577 CCTAAAGTCTAAGGCCCAACTATAAC
1 CCTAAAGACTAAGGCCCAACTATAAC
79603 C
1 C
79604 TTGCTCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (26 bp):
CCTAAAGACTAAGGCCCAACTATAAC
Found at i:82535 original size:36 final size:36
Alignment explanation
Indices: 82488--82582 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 36
82478 TCAAGGCAAG
* * * *
82488 GCAAACTTCTTCTGCATCAAGCAAAGCAA-ATCTGAA
1 GCAAAGTTCTTCTCCATCAAGCAAAGCAACAAC-AAA
82524 GCAAAGTTCTTCTCCATCAA-CAAAGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAAGCAAAGCAACAACAAA
* *
82559 GTAAAGTTCTTCTCCATAAAGCAA
1 GCAAAGTTCTTCTCCATCAAGCAA
82583 CAACAAAGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
35 28 0.55
36 23 0.45
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (36 bp):
GCAAAGTTCTTCTCCATCAAGCAAAGCAACAACAAA
Found at i:82583 original size:31 final size:32
Alignment explanation
Indices: 82526--82590 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
82516 AATCTGAAGC
82526 AAAGTTCTTCTCCATCAACAAAGCAACAACAAAGT
1 AAAGTTCTTCTCCAT--A-AAAGCAACAACAAAGT
82561 AAAGTTCTTCTCCAT-AAAGCAACAACAAAG
1 AAAGTTCTTCTCCATAAAAGCAACAACAAAG
82591 CTTACGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 15 0.50
35 15 0.50
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.20
Consensus pattern (32 bp):
AAAGTTCTTCTCCATAAAAGCAACAACAAAGT
Found at i:82964 original size:144 final size:144
Alignment explanation
Indices: 82704--82994 Score: 483
Period size: 144 Copynumber: 2.0 Consensus size: 144
82694 CAACCACTCC
* * *
82704 TTTGAAGATATGTCAAATCAATCTCAAATCTAGCAAATCCGACAACGAGAAATAACAAGGCTTCG
1 TTTGAAGATATATCAAATCAATCTCAAATCTAGCAAATCCGACAACAAGAAATAACAAGCCTTCG
* * *
82769 GCCATTCCTCTCAAATCCATTTCATCGAGATCAAGCTATCAAGCCCTCGAAAAGTTCCCAAGGAG
66 GCCATTCCTCTCAAATCCATTTCATCGAGATCAAGCTATCAAGCCCTCGAAAACTTCCAAACGAG
*
82834 ATCAAATTAGAGGA
131 ATCAAATCAGAGGA
* * *
82848 TTTGAAGATCTATCAAATCAATCTCAAATCTAGCAAATCCGACCACAAGGAATAACAAGCCTTCG
1 TTTGAAGATATATCAAATCAATCTCAAATCTAGCAAATCCGACAACAAGAAATAACAAGCCTTCG
82913 GCCATTCCTCTCAAATCCATTTCATCGAGATCAAGCTATCAAGCCCTCGAAAACTTCCAAACGAG
66 GCCATTCCTCTCAAATCCATTTCATCGAGATCAAGCTATCAAGCCCTCGAAAACTTCCAAACGAG
*
82978 ATCGAATCAGAGGA
131 ATCAAATCAGAGGA
82992 TTT
1 TTT
82995 TTTTTCACAT
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (144 bp):
TTTGAAGATATATCAAATCAATCTCAAATCTAGCAAATCCGACAACAAGAAATAACAAGCCTTCG
GCCATTCCTCTCAAATCCATTTCATCGAGATCAAGCTATCAAGCCCTCGAAAACTTCCAAACGAG
ATCAAATCAGAGGA
Found at i:86269 original size:25 final size:27
Alignment explanation
Indices: 86236--86298 Score: 94
Period size: 25 Copynumber: 2.4 Consensus size: 27
86226 ATTGATTACC
86236 CTTACTCTTTTTACTGATTACCA-TTT
1 CTTACTCTTTTTACTGATTACCATTTT
* *
86262 -TTACTCTTTTTAGTTATTACCATTTT
1 CTTACTCTTTTTACTGATTACCATTTT
86288 CTTACTCTTTT
1 CTTACTCTTTT
86299 CTTTTTACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 20 0.61
26 3 0.09
27 10 0.30
ACGTcount: A:0.17, C:0.21, G:0.03, T:0.59
Consensus pattern (27 bp):
CTTACTCTTTTTACTGATTACCATTTT
Found at i:86364 original size:35 final size:35
Alignment explanation
Indices: 86325--86437 Score: 138
Period size: 35 Copynumber: 3.1 Consensus size: 35
86315 ATTTTTTGCC
86325 TTTTTTACTTTAATTATTGAATACCATTTTTACTT
1 TTTTTTACTTTAATTATTGAATACCATTTTTACTT
* *
86360 TTTTTTACTTTAATTATTAAATACCATTTTTAATTAAT
1 TTTTTTACTTTAATTATTGAATACCATTTTT-ACT--T
** *
86398 TTTTTTA-TGTTAATTACCGAATACCATTTTTACTC
1 TTTTTTACT-TTAATTATTGAATACCATTTTTACTT
86433 TTTTT
1 TTTTT
86438 AATCTTTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
35 35 0.52
36 2 0.03
37 3 0.04
38 27 0.40
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (35 bp):
TTTTTTACTTTAATTATTGAATACCATTTTTACTT
Found at i:86485 original size:7 final size:7
Alignment explanation
Indices: 86475--86737 Score: 79
Period size: 7 Copynumber: 37.7 Consensus size: 7
86465 ATTTTACTGA
86475 TTACTCT
1 TTACTCT
86482 TTACTCT
1 TTACTCT
**
86489 TTACTGA
1 TTACTCT
*
86496 TTACT-A
1 TTACTCT
*
86502 TGAC-CAT
1 TTACTC-T
* *
86509 TTATTGT
1 TTACTCT
*
86516 TTACTGT
1 TTACTCT
86523 TTACTCTT
1 TTACTC-T
**
86531 TTACTGA
1 TTACTCT
*
86538 TTACT-A
1 TTACTCT
86544 TTACTCT
1 TTACTCT
86551 TT-CT-T
1 TTACTCT
86556 GATTACTCT
1 --TTACTCT
86565 TTACTCT
1 TTACTCT
**
86572 TTACTGA
1 TTACTCT
*
86579 CTA-T-T
1 TTACTCT
86584 ATTACTCT
1 -TTACTCT
86592 TT-CT-T
1 TTACTCT
86597 GATTACTCT
1 --TTACTCT
86606 TTACTCT
1 TTACTCT
86613 TTA--C-
1 TTACTCT
86617 TTACTACT
1 TTACT-CT
86625 ATTACTCTT
1 -TTACTC-T
86634 TTACTCT
1 TTACTCT
86641 TTACTC-
1 TTACTCT
86647 TTAC-CAT
1 TTACTC-T
**
86654 TTACTGA
1 TTACTCT
*
86661 TTGCTCT
1 TTACTCT
**
86668 TTAACTGA
1 TT-ACTCT
*
86676 TTACT-A
1 TTACTCT
86682 TTACTCTT
1 TTACTC-T
**
86690 TTACTGA
1 TTACTCT
86697 TTACTCT
1 TTACTCT
86704 TTACTCTT
1 TTACTC-T
**
86712 TTACTGA
1 TTACTCT
86719 TTACTCT
1 TTACTCT
*
86726 TCACTCT
1 TTACTCT
86733 TTACT
1 TTACT
86738 GATTCGTATT
Statistics
Matches: 191, Mismatches: 36, Indels: 58
0.67 0.13 0.20
Matches are distributed among these distances:
4 3 0.02
5 4 0.02
6 27 0.14
7 116 0.61
8 33 0.17
9 8 0.04
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.52
Consensus pattern (7 bp):
TTACTCT
Found at i:86491 original size:21 final size:21
Alignment explanation
Indices: 86467--86776 Score: 228
Period size: 21 Copynumber: 15.1 Consensus size: 21
86457 CCATTACCAT
86467 TTTACTGATTACTCTTTACTC
1 TTTACTGATTACTCTTTACTC
* *
86488 TTTACTGATTACT-ATGAC-C
1 TTTACTGATTACTCTTTACTC
* * *
86507 ATTTATTGTTTACTGTTTACTC
1 -TTTACTGATTACTCTTTACTC
*
86529 TTTTACTGATTACT-ATTACTC
1 -TTTACTGATTACTCTTTACTC
86550 TTT-CTTGATTACTCTTTACTC
1 TTTAC-TGATTACTCTTTACTC
*
86571 TTTACTGACTA-T-TATTACTC
1 TTTACTGATTACTCT-TTACTC
86591 TTT-CTTGATTACTCTTTACTC
1 TTTAC-TGATTACTCTTTACTC
* * *
86612 TTTACTTACTACT-ATTACTC
1 TTTACTGATTACTCTTTACTC
**
86632 TTTTACTCTTTACTC-TTAC-C
1 -TTTACTGATTACTCTTTACTC
*
86652 ATTTACTGATTGCTCTTTA---
1 -TTTACTGATTACTCTTTACTC
*
86671 ---ACTGATTACT-ATTACTC
1 TTTACTGATTACTCTTTACTC
86688 TTTTACTGATTACTCTTTACTC
1 -TTTACTGATTACTCTTTACTC
*
86710 TTTTACTGATTACTCTTCACTC
1 -TTTACTGATTACTCTTTACTC
*
86732 TTTACTGATT-CGT-ATTAC-C
1 TTTACTGATTAC-TCTTTACTC
86751 ATTTTACTGATTACTCTTTACTC
1 --TTTACTGATTACTCTTTACTC
86774 TTT
1 TTT
86777 GCCATTACCT
Statistics
Matches: 231, Mismatches: 30, Indels: 56
0.73 0.09 0.18
Matches are distributed among these distances:
14 3 0.01
15 9 0.04
19 5 0.02
20 62 0.27
21 104 0.45
22 47 0.20
23 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTACTGATTACTCTTTACTC
Found at i:86526 original size:41 final size:41
Alignment explanation
Indices: 86472--86776 Score: 235
Period size: 41 Copynumber: 7.5 Consensus size: 41
86462 ACCATTTTAC
* * *
86472 TGATTACTCTTTACTCTTTACTGATTACTATGAC-CATTTAT
1 TGATTACTCTTTACTCTTTACTGACTACTATTACTC-TTTCT
* * *
86513 TGTTTACTGTTTACTCTTTTACTGATTACTATTACTCTTTCT
1 TGATTACTCTTTACTC-TTTACTGACTACTATTACTCTTTCT
*
86555 TGATTACTCTTTACTCTTTACTGACTATTATTACTCTTTCT
1 TGATTACTCTTTACTCTTTACTGACTACTATTACTCTTTCT
*
86596 TGATTACTCTTTACTCTTTACTTACTACTATTA--C--TCT
1 TGATTACTCTTTACTCTTTACTGACTACTATTACTCTTTCT
* * *
86633 T--TTACTCTTTACTC-TTAC-CATTTACTGATTGCTCTTTAAC-
1 TGATTACTCTTTACTCTTTACTGA-CTACT-ATTACTCTTT--CT
* * *
86673 TGATTACT-ATTACTCTTTTACTGATTACTCTTTACTCTTT-T
1 TGATTACTCTTTACTC-TTTACTGACTACT-ATTACTCTTTCT
* *
86714 ACTGATTACTCTTCACTCTTTACTGA-TTCGTATTAC-CATTT-T
1 --TGATTACTCTTTACTCTTTACTGACTAC-TATTACTC-TTTCT
86756 ACTGATTACTCTTTACTCTTT
1 --TGATTACTCTTTACTCTTT
86777 GCCATTACCT
Statistics
Matches: 220, Mismatches: 23, Indels: 41
0.77 0.08 0.14
Matches are distributed among these distances:
33 1 0.00
34 8 0.04
35 16 0.07
37 5 0.02
39 2 0.01
40 1 0.00
41 76 0.35
42 70 0.32
43 35 0.16
44 6 0.03
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (41 bp):
TGATTACTCTTTACTCTTTACTGACTACTATTACTCTTTCT
Found at i:86726 original size:15 final size:14
Alignment explanation
Indices: 86676--86705 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
86666 CTTTAACTGA
86676 TTACTATTACTCTT
1 TTACTATTACTCTT
86690 TTACTGATTACTCTT
1 TTACT-ATTACTCTT
86705 T
1 T
86706 ACTCTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTACTATTACTCTT
Found at i:86793 original size:31 final size:31
Alignment explanation
Indices: 86755--86816 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
86745 ATTACCATTT
86755 TACTGATTACTCTTTACTCTTTGCCATTACC
1 TACTGATTACTCTTTACTCTTTGCCATTACC
86786 TACTGATTACTCTTTACTCTTTGCCATTACC
1 TACTGATTACTCTTTACTCTTTGCCATTACC
86817 ATTTGGCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (31 bp):
TACTGATTACTCTTTACTCTTTGCCATTACC
Found at i:87326 original size:23 final size:22
Alignment explanation
Indices: 87271--87333 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
87261 ACTCCTAAGT
*
87271 TCTAAATTAAATCTATAATTTAAA
1 TCTAAATGAAAT-TA-AATTTAAA
*
87295 T-TAATTGAAATTAAATTTAAA
1 TCTAAATGAAATTAAATTTAAA
87316 TCCTAAATGAAATTAAAT
1 T-CTAAATGAAATTAAAT
87334 CTTTAATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 9 0.26
22 2 0.06
23 22 0.65
24 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (22 bp):
TCTAAATGAAATTAAATTTAAA
Found at i:90432 original size:18 final size:18
Alignment explanation
Indices: 90399--90442 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
90389 AAACTGCACC
90399 CAAAAAAAATCCAAAAAGT
1 CAAAAAAAATCCAAAAA-T
*
90418 CAAAAAAAAT-GAAAAAT
1 CAAAAAAAATCCAAAAAT
*
90435 GAAAAAAA
1 CAAAAAAA
90443 TCTTACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.75, C:0.09, G:0.07, T:0.09
Consensus pattern (18 bp):
CAAAAAAAATCCAAAAAT
Found at i:90614 original size:204 final size:205
Alignment explanation
Indices: 90264--90648 Score: 718
Period size: 204 Copynumber: 1.9 Consensus size: 205
90254 GGGCTTTGAT
* *
90264 ATGGAAATGTAATGCAAATGCTAGATGAGTAAGATGTTTTCCAAATGGTTAAATCTACCAATGCA
1 ATGGAAATGTAATGCAAATGCTAGATGAGTAAGATGTTTTACAAATGGGTAAATCTACCAATGCA
90329 AAATAAGAATATATTCTAAATAAAAGGATACACAAAAATGGGGGTCTACAGCAAGAGCCTAAACT
66 AAATAAGAATATATTCTAAATAAAAGGATACACAAAAATGGGGGTCTACAGCAAGAGCCTAAACT
90394 GCACCCAAAAAAAATCCAAAAAGTC-AAAAAAAATGAAAAATGAAAAAAATCTTACTAGATGAGT
131 GCACCCAAAAAAAATCCAAAAAGTCAAAAAAAAATGAAAAATGAAAAAAATCTTACTAGATGAGT
90458 AAATCAACCA
196 AAATCAACCA
90468 ATGGAAATGTAATGCAAATGCTAGATGAGTAAGATGTTTTACAAATGGGTAAATCTACCAATGCA
1 ATGGAAATGTAATGCAAATGCTAGATGAGTAAGATGTTTTACAAATGGGTAAATCTACCAATGCA
*
90533 AAATAAGAATATATTCTAAATAAAAGGATACACAAAAATGGGTGTCTACAGCAAGAGCCTAAACT
66 AAATAAGAATATATTCTAAATAAAAGGATACACAAAAATGGGGGTCTACAGCAAGAGCCTAAACT
*
90598 GCACCCAAAAAAAATCCAAAAAGTCAAAAAAAAAATGAAAGATGAAAAAAA
131 GCACCCAAAAAAAATCCAAAAAGTC-AAAAAAAAATGAAAAATGAAAAAAA
90649 AAGTGAACTA
Statistics
Matches: 175, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
204 152 0.87
206 23 0.13
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.21
Consensus pattern (205 bp):
ATGGAAATGTAATGCAAATGCTAGATGAGTAAGATGTTTTACAAATGGGTAAATCTACCAATGCA
AAATAAGAATATATTCTAAATAAAAGGATACACAAAAATGGGGGTCTACAGCAAGAGCCTAAACT
GCACCCAAAAAAAATCCAAAAAGTCAAAAAAAAATGAAAAATGAAAAAAATCTTACTAGATGAGT
AAATCAACCA
Found at i:90638 original size:18 final size:19
Alignment explanation
Indices: 90617--90655 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
90607 AAAAATCCAA
90617 AAAG-TCAAAAAAAAAATG
1 AAAGATCAAAAAAAAAATG
* *
90635 AAAGATGAAAAAAAAAGTG
1 AAAGATCAAAAAAAAAATG
90654 AA
1 AA
90656 CTACGTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAGATCAAAAAAAAAATG
Found at i:90918 original size:47 final size:47
Alignment explanation
Indices: 90761--91281 Score: 630
Period size: 46 Copynumber: 11.2 Consensus size: 47
90751 CATGATCCCA
* * *
90761 CCAAGATGCCGATGTAGAGGTAGAGGGTGATAAGAAAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAA-AAAAATCAACCCCG
* * * * *
90809 TCAATAAACCGATGCAGAGGTAGAGGGCAAT-AAATAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* * * * * *
90855 CCAAGAGGCCGCTGCAGAGGTAGAGGGAGATAAAAGAATCAGCCCCA
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* * *
90902 CCAAGACGCTGATGCAGAGGTAGAGGGTGATAAAAAAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGAT-AAAAAAATCAACCCCG
* * * *
90950 CCAAGAAGCCGATGC-GAAAGTAGAGGGTGAT-AAATAATCAAACCCG
1 CCAAGAAGCCGATGCAG-AGGTAGAGGGCGATAAAAAAATCAACCCCG
*
90996 CCAAGAAGCCGAAGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* *
91043 CCAAGAGGCTGATGCAGAGGTAGAGGGCGAT-AAAAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* *
91089 CC-AGATGCCGATGTAGAGGTAGA-GGCTGAT-AAAAAATCAA-CCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGC-GATAAAAAAATCAACCCCG
* *
91133 CCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAAGCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* *
91180 CCAAGATGCCGATGCAGAGGTAGAGAGCGAT-AAAAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
* * * *
91226 CCAAGAGGCCGATGCAGAGGTAGAGGGTGACAAATAAATCAACCCCG
1 CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
91273 CCAA-AAGCC
1 CCAAGAAGCC
91282 AAACAAACAA
Statistics
Matches: 410, Mismatches: 52, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
44 9 0.02
45 53 0.13
46 151 0.37
47 134 0.33
48 63 0.15
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (47 bp):
CCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCG
Found at i:90935 original size:93 final size:92
Alignment explanation
Indices: 90761--91276 Score: 644
Period size: 93 Copynumber: 5.5 Consensus size: 92
90751 CATGATCCCA
* * * * * **
90761 CCAAGATGCCGATGTAGAGGTAGAGGGTGATAAGAAAAATCAACCCCGTCAATAAACCGATGCAG
1 CCAAGAGGCCGATGCAGAGGTAGAGGGCGAT-A-AAAAATCAACCCCGCCAAGATGCCGATGCAG
* *
90826 AGGTAGAGGGCAATAAATAATCAACCCCG
64 AGGTAGAGGGCGATAAAAAATCAACCCCG
* * * * * *
90855 CCAAGAGGCCGCTGCAGAGGTAGAGGGAGATAAAAGAATCAGCCCCACCAAGACGCTGATGCAGA
1 CCAAGAGGCCGATGCAGAGGTAGAGGGCGATAAAA-AATCAACCCCGCCAAGATGCCGATGCAGA
*
90920 GGTAGAGGGTGATAAAAAAAATCAACCCCG
65 GGTAGAGGGCGAT--AAAAAATCAACCCCG
* * * * * * *
90950 CCAAGAAGCCGATGC-GAAAGTAGAGGGTGATAAATAATCAAACCCGCCAAGAAGCCGAAGCAGA
1 CCAAGAGGCCGATGCAG-AGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGATGCCGATGCAGA
91014 GGTAGAGGGCGATAAAAAAATCAACCCCG
65 GGTAGAGGGCGAT-AAAAAATCAACCCCG
* *
91043 CCAAGAGGCTGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCC-AGATGCCGATGTAGAG
1 CCAAGAGGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGATGCCGATGCAGAG
91107 GTAGA-GGCTGATAAAAAATCAA-CCCG
66 GTAGAGGGC-GATAAAAAATCAACCCCG
* *
91133 CCAAGACGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAAGCCCGCCAAGATGCCGATGCAGA
1 CCAAGAGGCCGATGCAGAGGTAGAGGGCGAT-AAAAAATCAACCCCGCCAAGATGCCGATGCAGA
*
91198 GGTAGAGAGCGATAAAAAATCAACCCCG
65 GGTAGAGGGCGATAAAAAATCAACCCCG
* *
91226 CCAAGAGGCCGATGCAGAGGTAGAGGGTGACAAATAAATCAACCCCGCCAA
1 CCAAGAGGCCGATGCAGAGGTAGAGGGCGATAAA-AAATCAACCCCGCCAA
91277 AAGCCAAACA
Statistics
Matches: 367, Mismatches: 44, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
90 33 0.09
91 29 0.08
92 60 0.16
93 139 0.38
94 64 0.17
95 42 0.11
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (92 bp):
CCAAGAGGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGATGCCGATGCAGAG
GTAGAGGGCGATAAAAAATCAACCCCG
Found at i:90940 original size:141 final size:139
Alignment explanation
Indices: 90757--91281 Score: 666
Period size: 141 Copynumber: 3.8 Consensus size: 139
90747 CAGTCATGAT
* * * * *
90757 CCCACCAAGATGCCGATGTAGAGGTAGAGGGTGATAAGAAAAATCAACCCCGTCAATAAACCGAT
1 CCCACCAAGATGCCGATGCAGAGGTAGAGGGCGAT-A-AAAAATCAACCCCGCCAAGAAGCCGAT
* * * *
90822 GCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAAGAGGCCGCTGCAGAGGTAGAGGGAGATA
64 GCAGAGGTAGAGGGCGATAAATAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATA
*
90887 AAAGAATCAGC
129 AAAAAATCAGC
* * *
90898 CCCACCAAGACGCTGATGCAGAGGTAGAGGGTGATAAAAAAAATCAACCCCGCCAAGAAGCCGAT
1 CCCACCAAGATGCCGATGCAGAGGTAGAGGGCGAT--AAAAAATCAACCCCGCCAAGAAGCCGAT
* * * *
90963 GC-GAAAGTAGAGGGTGATAAATAATCAAACCCGCCAAGAAGCCGAAGCAGAGGTAGAGGGCGAT
64 GCAG-AGGTAGAGGGCGATAAATAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCGAT
*
91027 AAAAAAATCAAC
128 AAAAAAATCAGC
* * * * *
91039 CCCGCCAAGAGGCTGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCC-AGATGCCGATGT
1 CCCACCAAGATGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGC
* *
91103 AGAGGTAGA-GGCTGATAAAAAATCAA-CCCGCCAAGACGCCGATGCAGAGGTAGAGGGCGATAA
66 AGAGGTAGAGGGC-GATAAATAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAA
91166 AAAAATCAAG-
130 AAAAATC-AGC
* * *
91176 CCCGCCAAGATGCCGATGCAGAGGTAGAGAGCGATAAAAAATCAACCCCGCCAAGAGGCCGATGC
1 CCCACCAAGATGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGC
* *
91241 AGAGGTAGAGGGTGACAAATAAATCAACCCCGCCAA-AAGCC
66 AGAGGTAGAGGGCGATAAAT-AATCAACCCCGCCAAGAAGCC
91282 AAACAAACAA
Statistics
Matches: 339, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
137 93 0.27
138 53 0.16
139 30 0.09
140 9 0.03
141 152 0.45
142 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (139 bp):
CCCACCAAGATGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGC
AGAGGTAGAGGGCGATAAATAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAA
AAAATCAGC
Found at i:92101 original size:20 final size:20
Alignment explanation
Indices: 92076--92123 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
92066 GATCAAGCCC
92076 GAAGCCAAATAATTGGAAAA
1 GAAGCCAAATAATTGGAAAA
92096 GAAGCCAAATAATTGGAAAA
1 GAAGCCAAATAATTGGAAAA
92116 GAAGCCAA
1 GAAGCCAA
92124 GACATAGACT
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:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (20 bp):
GAAGCCAAATAATTGGAAAA
Found at i:93667 original size:21 final size:21
Alignment explanation
Indices: 93641--93682 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
93631 TCCTTTGGTG
* *
93641 ATGATCTCTAATGGGCTTCAA
1 ATGATCTCCAATGGCCTTCAA
93662 ATGATCTCCAATGGCCTTCAA
1 ATGATCTCCAATGGCCTTCAA
93683 CTCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
ATGATCTCCAATGGCCTTCAA
Found at i:93868 original size:21 final size:21
Alignment explanation
Indices: 93798--93856 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
93788 CTTAGGCAAT
*
93798 TCCAATGAGCTTGGAACCGTC
1 TCCAATGAGCTTGGAACCTTC
93819 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
93840 TCCAATGAGCTTGGAAC
1 TCCAATGAGCTTGGAAC
93857 TTATTCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:97225 original size:21 final size:20
Alignment explanation
Indices: 97201--97271 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 20
97191 CTTAGGCAAT
*
97201 TCCAATGAGCTTGAAATCTTC
1 TCCAATGAGCTTGGAA-CTTC
97222 TCCAAAT-AGCTTGGAACCTTC
1 TCC-AATGAGCTTGGAA-CTTC
97243 TCCAATGAGCTTGGAACTTTC
1 TCCAATGAGCTTGGAAC-TTC
97264 TCCAATGA
1 TCCAATGA
97272 ACTCCTAGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.09
21 38 0.84
22 3 0.07
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (20 bp):
TCCAATGAGCTTGGAACTTC
Found at i:98524 original size:35 final size:35
Alignment explanation
Indices: 98451--98589 Score: 171
Period size: 35 Copynumber: 4.1 Consensus size: 35
98441 TCAAGGCAAG
* * * *
98451 GCAAAGTTCTTATGCATCAAGCAAAGCAA-ATCTGAA
1 GCAAAGTTCTTCTCCATCAA-CAAAGCAACAAC-AAA
*
98487 GCAAATTTCTTCTCCATCAACAAAGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
*
98522 GCAAAGTTCTTCTCCATCAACAAAGAAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
98557 GCAAAGTTCTTCTCCAT----AAAGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
98588 GC
1 GC
98590 TTACGAAAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
31 15 0.16
35 60 0.64
36 19 0.20
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (35 bp):
GCAAAGTTCTTCTCCATCAACAAAGCAACAACAAA
Found at i:100434 original size:30 final size:32
Alignment explanation
Indices: 100381--100440 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
100371 TATAAGAAAG
*
100381 CCCTCAAACAATTCTATTTTATATGATTTAAA
1 CCCTCAAACAATTCTATTCTATATGATTTAAA
*
100413 CCCT-AAAC-ATTTTATTCTATATGATTTA
1 CCCTCAAACAATTCTATTCTATATGATTTA
100441 GTCATTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 18 0.69
31 4 0.15
32 4 0.15
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (32 bp):
CCCTCAAACAATTCTATTCTATATGATTTAAA
Found at i:101304 original size:36 final size:36
Alignment explanation
Indices: 101225--101319 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
101215 CTTTATGTCT
*
101225 TGTCCAACTTAACTCTCTTCTTG-TCACCTAGTTCA
1 TGTCCAACTTAACTCTCTTCTTGTTAACCTAGTTCA
* *
101260 TGTACAACTT-ACATCTCTTCTTGTTAACTTAGTTCA
1 TGTCCAACTTAAC-TCTCTTCTTGTTAACCTAGTTCA
101296 TGTCCAACTTAACTCTCTTCTTGT
1 TGTCCAACTTAACTCTCTTCTTGT
101320 CATGTGACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
34 2 0.04
35 19 0.36
36 30 0.57
37 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.43
Consensus pattern (36 bp):
TGTCCAACTTAACTCTCTTCTTGTTAACCTAGTTCA
Found at i:107366 original size:20 final size:20
Alignment explanation
Indices: 107343--107380 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
107333 TCCACAAACA
107343 GGTTAAAATGCTGACAAGCG
1 GGTTAAAATGCTGACAAGCG
*
107363 GGTTAAAATGTTGACAAG
1 GGTTAAAATGCTGACAAG
107381 TACATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGTTAAAATGCTGACAAGCG
Found at i:115513 original size:60 final size:60
Alignment explanation
Indices: 115361--115518 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 60
115351 CCCCGTACCG
** ** * *
115361 TTATTTGAGCATTTTTTATAAAATTAGACCCTTATTTAGCCAAATTAAAAGATCGGACTC
1 TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGACCC
* *
115421 TTATTTGAGCATTTTCGATAACGTTAAACCCTTATTTGGCCAAATTAAAAGATCGGGCCC
1 TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGACCC
* * *
115481 TTATTTGAGCATTTTGGCA-GACGTTAGGCCCTTATTTG
1 TTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTG
115519 AGCAATTAGC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 84 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGACCC
Found at i:116284 original size:29 final size:29
Alignment explanation
Indices: 116249--116348 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
116239 ATAACGTTAT
116249 ACCCTTATTTGGCCAAATTAAAAGATCGG
1 ACCCTTATTTGGCCAAATTAAAAGATCGG
** * **
116278 ACCCTTATTTGAG-CATTTTCGATAACG-TTAG
1 ACCCTTATTTG-GCCAAATT--A-AAAGATCGG
116309 ACCCTTATTTGGCCAAATTAAAAGATCGG
1 ACCCTTATTTGGCCAAATTAAAAGATCGG
**
116338 GTCCTTATTTG
1 ACCCTTATTTG
116349 AGCATTTTAG
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 27 0.51
30 2 0.04
31 18 0.34
32 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (29 bp):
ACCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:116295 original size:60 final size:60
Alignment explanation
Indices: 116217--116379 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
116207 ACTGACCCCA
* ** *
116217 GACCGTTATTTGAGCATTTTTTATAACGTTATACCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
116277 GACCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
** * *
116337 GGTCCTTATTTGAGCATTTTAGCA-AACGTTAGGCCCTTATTTG
1 GACCCTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTG
116380 AGTAATTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 93 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:116582 original size:861 final size:861
Alignment explanation
Indices: 114921--116644 Score: 2982
Period size: 861 Copynumber: 2.0 Consensus size: 861
114911 CAGAACAAAG
* * *
114921 TCCATGTGAAACCATTCGGAGAAATATTAGGGAAGAAGAAACCCACCCAAATAAAAATGAAGACA
1 TCCATGTGAAACCATTCAGAGAAATATTAGGAAAGAAGAAACCCACCCAAATAAAAATAAAGACA
*
114986 AAAGGAAAACAAAACTGAAATGTCAATAATTTAACCATGAATCAACCATTATTGCAGTTACATTT
66 AAAGGAAAACAAAACTGAAATGTCAATAATTTAACCATGAATCAACCATTATTGCAGATACATTT
* * *
115051 ATAGCACCAATCTTTTGGAATTCCGGCAGCGGAGTTGAGCTGGTAAATCTTCATATTTTCTCACT
131 ATAGCACCAATCTTTTGGAATTCCAGCAGCGGAGTTGAACTGATAAATCTTCATATTTTCTCACT
* * * *
115116 TTTGGAGTGACTAAAAAGTCCCTCGACGACTTTTCTCCCTTATTTTTCCTGCTACCCTTTTTTGT
196 TTTGGAGTGACTAAAAAGTCCCTCGACGAATTTCCTCCCTTACTTTTCCTGCTACCCTTTTTTGC
* *
115181 AATTTACTATTTTTATATTTAGGCTAATTGCTCAAATAATGGCCTAACGTTTGCCAAAATGCTCA
261 AATTTACTATTTTTATATTTAGGCTAATTGCTCAAATAATGACCTAACGATTGCCAAAATGCTCA
* *
115246 AATAAGGGCCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTTGCCAAAATACTTAGATAA
326 AATAAAGGCCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTTGCCAAAATACTTAAATAA
*
115311 GGGCCTGGCATCGAAAATTCTCACCTATCATCCAAACTGACCCCGTACCGTTATTTGAGCATTTT
391 GGGCCTGGAATCGAAAATTCTCACCTATCATCCAAACTGACCCCGTACCGTTATTTGAGCATTTT
*
115376 TTATAAAATTAGACCCTTATTTAGCCAAATTAAAAGATCGGACTCTTATTTGAGCATTTTCGATA
456 TTATAAAATTAGACCCTTATTTAGCCAAATTAAAAGATCGGACCCTTATTTGAGCATTTTCGATA
* *
115441 ACGTTAAACCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGGCAGACGTT
521 ACGTTAAACCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTAGCAAACGTT
115506 AGGCCCTTATTTGAGCAATTAGCCATTATATTTATGATTAAGTGTGTTTTAATTACATATTAATT
586 AGGCCCTTATTTGAGCAATTAGCCATTATATTTATGATTAAGTGTGTTTTAATTACATATTAATT
* * * *
115571 GTATTTACAAAAGGCTGAGGTAGTCTGATATATTAATTAAATCATCTATTCCCATTAAAAGAGAA
651 GTATTTACAAAAGGCTAAGATAGCCTGATATATTAATTAAATCATCTATTCCCATTAAAAGAAAA
*
115636 TTAGGATAATTTTGCAGTTTTAACTGATATAATATCCATTACTCAGTACCTTTTGCCAGGCCCTT
716 TTAGGATAATTTTGCAGTTTTAACTGATATAAGATCCATTACTCAGTACCTTTTGCCAGGCCCTT
115701 CTTATGCTTTGTTTGACATTTCCAACAGACTTGGCAAATACCTTGCAAATAGCCTGATAATATTG
781 CTTATGCTTTGTTTGACATTTCCAACAGACTTGGCAAATACCTTGCAAATAGCCTGATAATATTG
115766 TCAAAAATGCAAGAAA
846 TCAAAAATGCAAGAAA
*
115782 TCCATGTGAAACCATTCATAGAAATATTAGGAAAGAAGAAACCCACCCAAATAAAAATAAAGACA
1 TCCATGTGAAACCATTCAGAGAAATATTAGGAAAGAAGAAACCCACCCAAATAAAAATAAAGACA
* *
115847 AAAGGAAAACAGAACTGAAATGTCAGTAATTTAACCATGAATCAACCATTATTGCAGATACATTT
66 AAAGGAAAACAAAACTGAAATGTCAATAATTTAACCATGAATCAACCATTATTGCAGATACATTT
* * *
115912 ATAGCACGAATCTTTTGGAATTCCAGCAGCGGAGTTGAACTGATAAATCTTGATCTTTTCTCACT
131 ATAGCACCAATCTTTTGGAATTCCAGCAGCGGAGTTGAACTGATAAATCTTCATATTTTCTCACT
* * *
115977 TTTGGGGTGACTAAAAAGTCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCTGCCCTTTTTTGC
196 TTTGGAGTGACTAAAAAGTCCCTCGACGAATTTCCTCCCTTACTTTTCCTGCTACCCTTTTTTGC
* *
116042 AATTTATTATTTTTATATTTAGGTTAATTGCTCAAATAATGACCTAACGATTGCCAAAATGCTCA
261 AATTTACTATTTTTATATTTAGGCTAATTGCTCAAATAATGACCTAACGATTGCCAAAATGCTCA
* * *
116107 AATAAAGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAGCGTTTGCCAAAATGCTTAAATAA
326 AATAAAGGCCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTTGCCAAAATACTTAAATAA
*
116172 GGGCCTGGAATCGAAAATTCTCATCTATCATCCAAACTGACCCCAG-ACCGTTATTTGAGCATTT
391 GGGCCTGGAATCGAAAATTCTCACCTATCATCCAAACTGACCCC-GTACCGTTATTTGAGCATTT
** * *
116236 TTTATAACGTTATACCCTTATTTGGCCAAATTAAAAGATCGGACCCTTATTTGAGCATTTTCGAT
455 TTTATAAAATTAGACCCTTATTTAGCCAAATTAAAAGATCGGACCCTTATTTGAGCATTTTCGAT
* *
116301 AACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGGTCCTTATTTGAGCATTTTAGCAAACGT
520 AACGTTAAACCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTAGCAAACGT
*
116366 TAGGCCCTTATTTGAGTAATTAGCCATTATATTTATGATTAAGTGTGTTTTAATTACATATTAAT
585 TAGGCCCTTATTTGAGCAATTAGCCATTATATTTATGATTAAGTGTGTTTTAATTACATATTAAT
*
116431 TGTGTTTACAAAAGGCTAAGATAGCCTGATATATTAATTAAATCATCTATTCCCATTAAAAGAAA
650 TGTATTTACAAAAGGCTAAGATAGCCTGATATATTAATTAAATCATCTATTCCCATTAAAAGAAA
* *
116496 ATTGGGATAATTTTGCAGTTTTAACTGATATGAGATCCATTACTCAGTACCTTTTGCCAGGCCCT
715 ATTAGGATAATTTTGCAGTTTTAACTGATATAAGATCCATTACTCAGTACCTTTTGCCAGGCCCT
*
116561 TCTTATGCTTTGTTTGACATTTTCAACAGACTTGGCAAATACCTTGCAAATAGCCTGATAATATT
780 TCTTATGCTTTGTTTGACATTTCCAACAGACTTGGCAAATACCTTGCAAATAGCCTGATAATATT
116626 GTCAAAAATGCAAGAAA
845 GTCAAAAATGCAAGAAA
116643 TC
1 TC
116645 TTAAGCAATC
Statistics
Matches: 812, Mismatches: 50, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
861 811 1.00
862 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (861 bp):
TCCATGTGAAACCATTCAGAGAAATATTAGGAAAGAAGAAACCCACCCAAATAAAAATAAAGACA
AAAGGAAAACAAAACTGAAATGTCAATAATTTAACCATGAATCAACCATTATTGCAGATACATTT
ATAGCACCAATCTTTTGGAATTCCAGCAGCGGAGTTGAACTGATAAATCTTCATATTTTCTCACT
TTTGGAGTGACTAAAAAGTCCCTCGACGAATTTCCTCCCTTACTTTTCCTGCTACCCTTTTTTGC
AATTTACTATTTTTATATTTAGGCTAATTGCTCAAATAATGACCTAACGATTGCCAAAATGCTCA
AATAAAGGCCCGATCTTTTAATTTGACCAAATAAGGGCCTAACGTTTGCCAAAATACTTAAATAA
GGGCCTGGAATCGAAAATTCTCACCTATCATCCAAACTGACCCCGTACCGTTATTTGAGCATTTT
TTATAAAATTAGACCCTTATTTAGCCAAATTAAAAGATCGGACCCTTATTTGAGCATTTTCGATA
ACGTTAAACCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTAGCAAACGTT
AGGCCCTTATTTGAGCAATTAGCCATTATATTTATGATTAAGTGTGTTTTAATTACATATTAATT
GTATTTACAAAAGGCTAAGATAGCCTGATATATTAATTAAATCATCTATTCCCATTAAAAGAAAA
TTAGGATAATTTTGCAGTTTTAACTGATATAAGATCCATTACTCAGTACCTTTTGCCAGGCCCTT
CTTATGCTTTGTTTGACATTTCCAACAGACTTGGCAAATACCTTGCAAATAGCCTGATAATATTG
TCAAAAATGCAAGAAA
Found at i:117425 original size:2 final size:2
Alignment explanation
Indices: 117418--117452 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
117408 CGCCATACTG
117418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117453 GTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.