Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020602.1 Corchorus olitorius cultivar O-4 contig20635, 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: 102365
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2458 original size:21 final size:20
Alignment explanation
Indices: 2426--2481 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
2416 AAATCTTAAT
2426 AAGTATTTTAGTGACCTCATA
1 AAGT-TTTTAGTGACCTCATA
* * * *
2447 AAGTTTTATAGTAACTTCTTT
1 AAGTTTT-TAGTGACCTCATA
2468 AAGTTTTTAGTGAC
1 AAGTTTTTAGTGAC
2482 ATTATCAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
AAGTTTTTAGTGACCTCATA
Found at i:4061 original size:20 final size:18
Alignment explanation
Indices: 4022--4061 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
4012 CTAGCCCTAA
*
4022 AACTAGAAGAAAAAATAG
1 AACTAGAAGAAAAAAAAG
4040 AACTAGAAGAGAAAAAGAAG
1 AACTAGAAGA-AAAAA-AAG
4060 AA
1 AA
4062 GAGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.20, T:0.07
Consensus pattern (18 bp):
AACTAGAAGAAAAAAAAG
Found at i:4694 original size:19 final size:18
Alignment explanation
Indices: 4661--4696 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4651 TTGAGATAAT
4661 TCTTCAATAGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
*
4679 TCTTCAAATTGTCTTCAA
1 TCTTC-AATAGTCTTCAA
4697 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:8149 original size:24 final size:24
Alignment explanation
Indices: 8122--8167 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
8112 TGAAAACGCA
8122 AAAACAAGAATTTTTTTT-TATCAT
1 AAAACAA-AATTTTTTTTATATCAT
* *
8146 AAAACCATATTTTTTTTATATC
1 AAAACAAAATTTTTTTTATATC
8168 GCAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (24 bp):
AAAACAAAATTTTTTTTATATCAT
Found at i:9264 original size:20 final size:18
Alignment explanation
Indices: 9225--9260 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9215 CTAGCCCTAA
*
9225 AACTAGAAGAAAAACGAG
1 AACTAGAAGAAAAAAGAG
9243 AACTAGAAGAGAAAAAGA
1 AACTAGAAGA-AAAAAGA
9261 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:0.22, T:0.06
Consensus pattern (18 bp):
AACTAGAAGAAAAAAGAG
Found at i:11362 original size:18 final size:17
Alignment explanation
Indices: 11324--11374 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
11314 AGGGAATATT
*
11324 AATAATAATTATTCTGAA
1 AATAATAATTATT-TAAA
11342 AATAATAATTATTTAATA
1 AATAATAATTATTTAA-A
*
11360 AATTATTAATTATTT
1 AA-TAATAATTATTT
11375 TTGGCCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 16 0.55
19 11 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
AATAATAATTATTTAAA
Found at i:21243 original size:12 final size:11
Alignment explanation
Indices: 21227--21283 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 11
21217 TTATGCATCC
21227 AAAACATTTAT
1 AAAACATTTAT
21238 CAAAACATTTTAT
1 -AAAACA-TTTAT
*
21251 AAATCATTTATGT
1 AAAACATTTA--T
* *
21264 AAAACAGTAAT
1 AAAACATTTAT
21275 AAAACATTT
1 AAAACATTT
21284 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 12 0.33
12 11 0.31
13 13 0.36
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:28457 original size:25 final size:25
Alignment explanation
Indices: 28428--28476 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28418 TTTTAAAAGT
28428 CATAGAATCTGCCATAAAACTAAAA
1 CATAGAATCTGCCATAAAACTAAAA
* *
28453 CATAGAGTCTGTCATAAAACTAAA
1 CATAGAATCTGCCATAAAACTAAA
28477 GTCTAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.22
Consensus pattern (25 bp):
CATAGAATCTGCCATAAAACTAAAA
Found at i:28563 original size:18 final size:19
Alignment explanation
Indices: 28527--28567 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
28517 TTTTTATTGA
28527 TATTTTTTTATTAAATTATG
1 TATTTTTTTATT-AATTATG
*
28547 TATTTTTTTATT-GTTATG
1 TATTTTTTTATTAATTATG
28565 TAT
1 TAT
28568 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
TATTTTTTTATTAATTATG
Found at i:32277 original size:28 final size:30
Alignment explanation
Indices: 32246--32321 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 30
32236 TCCAAATTGC
*
32246 AAGTTCAGGGGGC-AAACGTCCACAAT-TA-
1 AAGTTCAGGGGGCAAAACGT-CAAAATATAG
* *
32274 AAGTTTATGGGGCAAAACGTCAAAATCATAG
1 AAGTTCAGGGGGCAAAACGTCAAAAT-ATAG
*
32305 AAGTTCAGGGGGTAAAA
1 AAGTTCAGGGGGCAAAA
32322 AGGGCATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 16 0.42
29 6 0.16
30 2 0.05
31 14 0.37
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCAAAATATAG
Found at i:48855 original size:33 final size:33
Alignment explanation
Indices: 48818--48890 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
48808 GCTATAGAAC
48818 ACTCAAAACCCAATTCAACAAATACAAAATTAA
1 ACTCAAAACCCAATTCAACAAATACAAAATTAA
48851 ACTCAAAACCCAATTCAACAAATACAAAATTAA
1 ACTCAAAACCCAATTCAACAAATACAAAATTAA
48884 ACTCAAA
1 ACTCAAA
48891 CCCCCCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.18
Consensus pattern (33 bp):
ACTCAAAACCCAATTCAACAAATACAAAATTAA
Found at i:55845 original size:21 final size:21
Alignment explanation
Indices: 55820--55869 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
55810 GTGGCCATTT
55820 TCACCATCATTAACTCCCTGA
1 TCACCATCATTAACTCCCTGA
*
55841 TCACCATCATTAACTCCCTGT
1 TCACCATCATTAACTCCCTGA
55862 TCACCATC
1 TCACCATC
55870 TTGGCCATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.40, G:0.04, T:0.30
Consensus pattern (21 bp):
TCACCATCATTAACTCCCTGA
Found at i:57211 original size:27 final size:26
Alignment explanation
Indices: 57156--57212 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
57146 TTATGTCATC
*
57156 ATTAAAATATATATAAAATTTATATT
1 ATTAAAATATATATAAAATTTATAAT
*
57182 ATTAAAATATA-ATATAATTTCAATAAT
1 ATTAAAATATATATAAAATTT--ATAAT
57209 ATTA
1 ATTA
57213 TGTTTTTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 11 0.41
27 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAAAATATATATAAAATTTATAAT
Found at i:61273 original size:22 final size:22
Alignment explanation
Indices: 61246--61295 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
61236 GGAAGCTATT
*
61246 AAAATTTCATAGAGTGATTATC
1 AAAATTTCATAGAGAGATTATC
* *
61268 ATAATTTCATAGAGAGGTTATC
1 AAAATTTCATAGAGAGATTATC
61290 AAAATT
1 AAAATT
61296 CCAAAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGAGAGATTATC
Found at i:63873 original size:19 final size:19
Alignment explanation
Indices: 63829--63873 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
63819 GCACGGGTGG
* *
63829 TATTATGTATTATTAGTCT
1 TATTATTTATTATTAATCT
* *
63848 TAGTATTTATTATTAATGT
1 TATTATTTATTATTAATCT
63867 TATTATT
1 TATTATT
63874 ATTTATAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (19 bp):
TATTATTTATTATTAATCT
Found at i:67142 original size:45 final size:45
Alignment explanation
Indices: 67057--67145 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
67047 CTCTCTCACT
** *
67057 CTCCCTCTGAATCTGAGCAGCAGCAGCAGCCTCTGACTCCCTCTG
1 CTCCCTCTGAATCTGAGCAGCAGCAGCAGCAGCAGACTCCCTCTG
* * * *
67102 CTCCCTCTGACTGTGAGCAGCAGCAGCAGTAGCAGCCTCCCTCT
1 CTCCCTCTGAATCTGAGCAGCAGCAGCAGCAGCAGACTCCCTCT
67146 CCCTATAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (45 bp):
CTCCCTCTGAATCTGAGCAGCAGCAGCAGCAGCAGACTCCCTCTG
Found at i:67724 original size:16 final size:16
Alignment explanation
Indices: 67703--67779 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
67693 TTGAGGATTT
*
67703 GTTGAAGAAATTGAAG
1 GTTGAAGAAAATGAAG
**
67719 GTTGAAGAAGTTTGAAG
1 GTTGAAGAA-AATGAAG
*
67736 AAGTTGTTAGAAAATGAA-
1 --GTTG-AAGAAAATGAAG
*
67754 GTTGTTAGAAAATGAAG
1 GTTG-AAGAAAATGAAG
67771 GTTGAAGAA
1 GTTGAAGAA
67780 GTTTGAGAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 29 0.57
17 10 0.20
19 8 0.16
20 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (16 bp):
GTTGAAGAAAATGAAG
Found at i:67753 original size:19 final size:19
Alignment explanation
Indices: 67731--67770 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
67721 TGAAGAAGTT
67731 TGAAGAAGTTGTTAGAAAA
1 TGAAGAAGTTGTTAGAAAA
67750 T---GAAGTTGTTAGAAAA
1 TGAAGAAGTTGTTAGAAAA
67766 TGAAG
1 TGAAG
67771 GTTGAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 6
0.75 0.00 0.25
Matches are distributed among these distances:
16 16 0.89
19 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
TGAAGAAGTTGTTAGAAAA
Found at i:70726 original size:52 final size:51
Alignment explanation
Indices: 70648--70751 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 51
70638 GGACCTACTA
*
70648 AACCCAGGTGCTGGATGCGGGTTGAATTCGGGTTAATCGGAGCAAAACTCTG
1 AACCCAGGTGCTGGATGCGGGTTGAATCCGGGTTAATCGGAGCAAAAC-CTG
70700 AACCCAGGTGCTGGATGCGGGTTGAATCCGGGTTAATCGGAGCAAAACCTG
1 AACCCAGGTGCTGGATGCGGGTTGAATCCGGGTTAATCGGAGCAAAACCTG
70751 A
1 A
70752 GAAAAAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 4 0.08
52 47 0.92
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (51 bp):
AACCCAGGTGCTGGATGCGGGTTGAATCCGGGTTAATCGGAGCAAAACCTG
Found at i:75049 original size:12 final size:12
Alignment explanation
Indices: 75032--75076 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
75022 TACGGTCCGG
75032 GCTGCGGCTGTA
1 GCTGCGGCTGTA
*
75044 GCTGCGGCT-TGG
1 GCTGCGGCTGT-A
*
75056 GCTCCGGCTGTA
1 GCTGCGGCTGTA
75068 GCTGCGGCT
1 GCTGCGGCT
75077 ACGACCACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.04, C:0.29, G:0.42, T:0.24
Consensus pattern (12 bp):
GCTGCGGCTGTA
Found at i:75063 original size:24 final size:24
Alignment explanation
Indices: 75030--75076 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
75020 ACTACGGTCC
*
75030 GGGCTGCGGCTGTAGCTGCGGCTT
1 GGGCTCCGGCTGTAGCTGCGGCTT
75054 GGGCTCCGGCTGTAGCTGCGGCT
1 GGGCTCCGGCTGTAGCTGCGGCT
75077 ACGACCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.28, G:0.45, T:0.23
Consensus pattern (24 bp):
GGGCTCCGGCTGTAGCTGCGGCTT
Found at i:75107 original size:6 final size:6
Alignment explanation
Indices: 75096--75120 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
75086 TGACCAGCTC
75096 CTGCTT CTGCTT CTGCTT CTGCTT C
1 CTGCTT CTGCTT CTGCTT CTGCTT C
75121 GGCCACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.16, T:0.48
Consensus pattern (6 bp):
CTGCTT
Found at i:75466 original size:33 final size:33
Alignment explanation
Indices: 75429--75507 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
75419 ACCACTGAAG
*
75429 CCACCATCCCTCATACTGCCACGCCCACCAAAA
1 CCACCATCCCTCATACCGCCACGCCCACCAAAA
* * ** *
75462 CCACCATCTCTCATACCGCCACGGCTGCCAAAG
1 CCACCATCCCTCATACCGCCACGCCCACCAAAA
75495 CCACCATCCCTCA
1 CCACCATCCCTCA
75508 GTCCACCACG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.27, C:0.51, G:0.09, T:0.14
Consensus pattern (33 bp):
CCACCATCCCTCATACCGCCACGCCCACCAAAA
Found at i:83053 original size:16 final size:16
Alignment explanation
Indices: 83032--83063 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
83022 GTCAAACACT
83032 CTACCACTAAATCACA
1 CTACCACTAAATCACA
83048 CTACCACTAAATCACA
1 CTACCACTAAATCACA
83064 TGTATAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (16 bp):
CTACCACTAAATCACA
Found at i:86244 original size:33 final size:33
Alignment explanation
Indices: 86202--86269 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
86192 GTGAATGCCA
*
86202 TAGTAGTGGAACTTCAAATAATATGAAAGATAT
1 TAGTAGTGGAACTTCAAATAATATGAAAGACAT
86235 TAGTAGTGGAACTTCAAATAATATGAAAGACAT
1 TAGTAGTGGAACTTCAAATAATATGAAAGACAT
86268 TA
1 TA
86270 CAAAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (33 bp):
TAGTAGTGGAACTTCAAATAATATGAAAGACAT
Found at i:88532 original size:24 final size:25
Alignment explanation
Indices: 88473--88538 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
88463 TACGATGTCT
* *
88473 AAGGGTGAACAAAGCTCTTCCAAGTCC
1 AAGGTTGAACAAAGCACTTCCAAG--C
88500 AAGGTTGAACAAAGCACTTCCAAG-
1 AAGGTTGAACAAAGCACTTCCAAGC
*
88524 AAGGTTGAAAAAAGC
1 AAGGTTGAACAAAGC
88539 GAACATATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.39
27 22 0.61
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (25 bp):
AAGGTTGAACAAAGCACTTCCAAGC
Found at i:91835 original size:106 final size:106
Alignment explanation
Indices: 91718--91936 Score: 429
Period size: 106 Copynumber: 2.1 Consensus size: 106
91708 TGAAACATGT
91718 AATTAATGTTTGATATTGTTGTAGAAAAATATGGTTAAGAGATAAAATGTTTAAAAAAGGTGCTA
1 AATTAATGTTTGATATTGTTGTAGAAAAATATGGTTAAGAGATAAAATGTTTAAAAAAGGTGCTA
91783 ATTAAAATAGAAATAGAAAAAATATTTAAGAGAATTTAGTC
66 ATTAAAATAGAAATAGAAAAAATATTTAAGAGAATTTAGTC
91824 AATTAATGTTTGATATTGTTGTAGAAAAATATGGTTAAGAGATAAAATGTTTAAAAAAGGTGCTA
1 AATTAATGTTTGATATTGTTGTAGAAAAATATGGTTAAGAGATAAAATGTTTAAAAAAGGTGCTA
91889 ATTAAAATAGAAATAGAAAAAATATTTAAGAGAATTTAGTC
66 ATTAAAATAGAAATAGAAAAAATATTTAAGAGAATTTAGTC
*
91930 ATTTAAT
1 AATTAAT
91937 ATCCAAAACC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (106 bp):
AATTAATGTTTGATATTGTTGTAGAAAAATATGGTTAAGAGATAAAATGTTTAAAAAAGGTGCTA
ATTAAAATAGAAATAGAAAAAATATTTAAGAGAATTTAGTC
Found at i:91986 original size:19 final size:19
Alignment explanation
Indices: 91962--91999 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
91952 TGAAACGCAA
91962 AAACACCTAAAGATTAGCT
1 AAACACCTAAAGATTAGCT
91981 AAACACCTAAAGATTAGCT
1 AAACACCTAAAGATTAGCT
92000 TTTGAGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (19 bp):
AAACACCTAAAGATTAGCT
Found at i:92862 original size:17 final size:16
Alignment explanation
Indices: 92829--92867 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
92819 TCATTTTCAT
**
92829 TTTCATTGTATTGGAG
1 TTTCATTGTATCAGAG
92845 TTCTCATTGTATCAGAG
1 TT-TCATTGTATCAGAG
92862 TTTCAT
1 TTTCAT
92868 ACAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (16 bp):
TTTCATTGTATCAGAG
Found at i:95239 original size:2 final size:2
Alignment explanation
Indices: 95232--95262 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
95222 GTGAGTTAAT
*
95232 GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
95263 CCTACTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:96159 original size:26 final size:26
Alignment explanation
Indices: 96128--96181 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
96118 ATTTGTTACC
*
96128 ACTTACCAGGATATCTCTTGTTAGAT
1 ACTTACCAGGATATCTCCTGTTAGAT
96154 ACTTACCAGGATATCTCCTGTTAGAT
1 ACTTACCAGGATATCTCCTGTTAGAT
96180 AC
1 AC
96182 AAATTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (26 bp):
ACTTACCAGGATATCTCCTGTTAGAT
Found at i:100036 original size:42 final size:42
Alignment explanation
Indices: 99966--100132 Score: 173
Period size: 42 Copynumber: 4.1 Consensus size: 42
99956 CGTATGAAAA
*
99966 TAACACCTGAAAATGTTAGAATCAGCCAA-CTAATATAATTTG
1 TAACGCCTGAAAATGTTAGAATCAGCCAATC-AATATAATTTG
* * * *
100008 TAACGCTTGAGAATGTTAGAATTAGCCAATCAATA-CA---G
1 TAACGCCTGAAAATGTTAGAATCAGCCAATCAATATAATTTG
** * * *
100046 TGCCGCCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTG
1 TAACGCCTGAAAATGTTAGAATCAGCCAATCAATATAATTTG
* * *
100088 TAACGCCTGAAAATGTTAAAATCAACCAATCAATATAATCTG
1 TAACGCCTGAAAATGTTAGAATCAGCCAATCAATATAATTTG
100130 TAA
1 TAA
100133 TGTATGAAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
38 30 0.30
39 1 0.01
41 1 0.01
42 67 0.67
43 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (42 bp):
TAACGCCTGAAAATGTTAGAATCAGCCAATCAATATAATTTG
Found at i:100104 original size:80 final size:80
Alignment explanation
Indices: 99971--100122 Score: 232
Period size: 80 Copynumber: 1.9 Consensus size: 80
99961 GAAAATAACA
* * * * * * * *
99971 CCTGAAAATGTTAGAATCAGCCAACTAATATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCA
1 CCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTGTAACGCCTGAAAATGTTAAAATCAACCA
100036 ATCAATACAGTGCCG
66 ATCAATACAGTGCCG
100051 CCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTGTAACGCCTGAAAATGTTAAAATCAACCA
1 CCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTGTAACGCCTGAAAATGTTAAAATCAACCA
100116 ATCAATA
66 ATCAATA
100123 TAATCTGTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (80 bp):
CCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTGTAACGCCTGAAAATGTTAAAATCAACCA
ATCAATACAGTGCCG
Found at i:100172 original size:59 final size:59
Alignment explanation
Indices: 100088--100234 Score: 204
Period size: 59 Copynumber: 2.5 Consensus size: 59
100078 ATAAAATTTG
* * * * *
100088 TAACGCCTGAAAATGTTAAAATCAACCAATCAATATAATCTGTAATGTATGAAAATCAG
1 TAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAA
**
100147 TGTCGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAA
1 TAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAA
* * *
100206 TAACGCCTAAAAATATTAGAATCAGCCAA
1 TAACGCCTGAAAATGTTAGAATCAACCAA
100235 CTAGTATAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 76 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (59 bp):
TAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAA
Found at i:100348 original size:59 final size:59
Alignment explanation
Indices: 100251--100363 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
100241 TAATTAATTT
* * * * *
100251 GTAACATCTGAAAATGTTAGAATTAGCCAATCAATACAATTCGTAACGCATGAATATCA
1 GTAACACCAGAAAATGTCAGAATCAGCCAACCAATACAATTCGTAACGCATGAATATCA
* * * *
100310 GTAACACCAGAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAA
1 GTAACACCAGAAAATGTCAGAATCAGCCAACCAATACAATTCGTAACGCATGAA
100364 AATGTTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (59 bp):
GTAACACCAGAAAATGTCAGAATCAGCCAACCAATACAATTCGTAACGCATGAATATCA
Found at i:100398 original size:101 final size:104
Alignment explanation
Indices: 100150--100435 Score: 375
Period size: 101 Copynumber: 2.8 Consensus size: 104
100140 AAATCAGTGT
*
100150 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAATAACGCCTA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCC-A
* * *
100215 -AAAATATTAGAATCAGCCAACTAGTATAATTAATTTGTAA
65 GAAAATGTTAGAATCAGCCAACCAG-ATAATCAATTTGTAA
** * * * *
100255 CATCTGAAAATGTTAGAATTAGCCAATCAATACAAT-TCGTAACGCATGAATATCAGTAACACCA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCT-GTAACGCATGAAAATCAGTAACGCCA
* *
100319 GAAACTGTCAGAATCAGCCAACCAG-T-A-CAATTTGTAA
65 GAAAATGTTAGAATCAGCCAACCAGATAATCAATTTGTAA
* * *
100356 CGCCTGAAAATGTTAAAATCAACCAATTAATACAATCTGTAACGCATGAAAATCAGTAACGCCTG
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCAG
100421 AAAATGTTAGAATCA
66 AAAATGTTAGAATCA
100436 ACACATCAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
101 76 0.49
102 2 0.01
103 1 0.01
104 2 0.01
105 74 0.48
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (104 bp):
CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCAG
AAAATGTTAGAATCAGCCAACCAGATAATCAATTTGTAA
Found at i:100409 original size:17 final size:17
Alignment explanation
Indices: 100389--100425 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
100379 CAATTAATAC
*
100389 AATCTGTAACGCATGAA
1 AATCAGTAACGCATGAA
*
100406 AATCAGTAACGCCTGAA
1 AATCAGTAACGCATGAA
100423 AAT
1 AAT
100426 GTTAGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (17 bp):
AATCAGTAACGCATGAA
Found at i:100449 original size:101 final size:100
Alignment explanation
Indices: 100150--100467 Score: 368
Period size: 101 Copynumber: 3.1 Consensus size: 100
100140 AAATCAGTGT
* *
100150 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAATAACGCCTA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTG
* *
100215 AAAATATTAGAATCAGCCAACTAGTATAATTAATTTGTAA
66 AAAATGTTAGAATCAGCCAAC-A--AT-A-CAATTTGTAA
** * * * * *
100255 CATCTGAAAATGTTAGAATTAGCCAATCAATACAAT-TCGTAACGCATGAATATCAGTAACACCA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCT-GTAACGCATGAAAATCAGTAACGCCT
* * *
100319 GAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAA
65 GAAAATGTTAGAATCAGCCAA-CAATACAATTTGTAA
* *
100356 CGCCTGAAAATGTTAAAATCAACCAATTAATACAATCTGTAACGCATGAAAATCAGTAACGCCTG
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTG
* * *
100421 AAAATGTTAGAATCAACACATCAATACAATCTGTAA
66 AAAATGTTAGAATCAGC-CAACAATACAATTTGTAA
**
100457 CGTATGAAAAT
1 CGCCTGAAAAT
100468 CAGTAACGCC
Statistics
Matches: 178, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
101 99 0.56
102 4 0.02
103 1 0.01
104 1 0.01
105 72 0.40
106 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.25
Consensus pattern (100 bp):
CGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTG
AAAATGTTAGAATCAGCCAACAATACAATTTGTAA
Found at i:100450 original size:160 final size:160
Alignment explanation
Indices: 100258--101245 Score: 548
Period size: 160 Copynumber: 6.2 Consensus size: 160
100248 TTTGTAACAT
* * *
100258 CTGAAAATGTTAGAATTAGCCAATCAATACAAT-TCGTAACGCATGAATATCAGTAACACCAGAA
1 CTGAAAATGTTAGAATCAACCAATCAATACAATCT-GTAACGCATGAAAATCAGTAACACCAGAA
* * *
100322 ACT-GTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATTAA
65 AATGGT-AGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAA
*
100386 TACAATCTGTAACGCATGAAAATCAGTAACGC
129 TACAATATGTAACGCATGAAAATCAGTAACGC
* * *
100418 CTGAAAATGTTAGAATCAA-CACATCAATACAATCTGTAACGTATGAAAATCAGTAACGCCTGAA
1 CTGAAAATGTTAGAATCAACCA-ATCAATACAATCTGTAACGCATGAAAATCAGTAACACCAGAA
* * * * * * *
100482 AATGGTAGAATCAACCAACTAGTATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAAT
65 AATGGTAGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAAT
100547 ACAATATGTAACGCATGAAAATCAGTAACGC
130 ACAATATGTAACGCATGAAAATCAGTAACGC
* * * ** * ** * * * *
100578 CTGAAAATGCTAGAATCAGCCAACCCGTACAATTTGTTGCGCCTAAAAAT--GTTAAAATCA-AC
1 CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAG-TAACACCAGA-
* ** * *** * * * * *
100640 CAATAAATACAATC-TGTAACACA-TGAAAATTAGTAATGCCTAAAAATGTTAGAATCAACCAAT
64 AAAT-GGTAGAATCAACCAAC-CAGT-ACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAAT
* * * *
100703 CAATACAATCTGTAACACATGAAAATCAATGACGC
126 CAATACAATATGTAACGCATGAAAATCAGTAACGC
* * * * * ** ****
100738 CTAAAAATGTTAGAATTAGCCAA-C--T---A-GTGT-A---AT--TAATTTGTAACGTTTGAAA
1 CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACACCAGAAA
* * * * * * * * *** * **
100790 ATGTTAGAATTAGCCAATCAATACAATTTGTAACACATGAATATCAG-TAACGCCTGA--AATTG
66 ATGGTAGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAAT--GTTAAAATC-AACCAATCA
* * * * **
100852 TTAGAATCA-GCCAAC-CA-GTACAATTTGTAACGC
128 ATACAAT-ATG-TAACGCATG-AAAATCAGTAACGC
* * * *
100885 CTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGGAA
1 CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACACCAGAAA
* * * * ** ** *
100950 ATGTTAGAATCAACCAATCAATACAATCTGTAACGTATGAAAATCAG-TAACGCTTGAA--AAT-
66 ATGGTAGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAAT--GTTAA--AATCAACCAATC
** * *** * * **
101011 GTTATAATCAACCAAC-TA-GTATAATTTGTAACGC
127 AATACAAT-ATGTAACGCATG-AAAATCAGTAACGC
* * * * * * **
101045 TTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAAATCAGTAACGCTTGAA
1 CTGAAAATGTTAGAATCAACCAATCAATAC-AATCTGTAACGCATGAAAATCAGTAACACCAGAA
* * *
101110 AATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAAT
65 AATGGTAGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAAT
* *
101175 ACAATCTATAACGCATGAAAATCAGTAACGC
130 ACAATATGTAACGCATGAAAATCAGTAACGC
101206 CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAAC
1 CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAAC
101246 AAGAGCTGTT
Statistics
Matches: 633, Mismatches: 152, Indels: 86
0.73 0.17 0.10
Matches are distributed among these distances:
146 1 0.00
147 64 0.10
148 17 0.03
149 5 0.01
150 1 0.00
153 4 0.01
154 4 0.01
155 1 0.00
157 1 0.00
158 7 0.01
159 15 0.02
160 388 0.61
161 123 0.19
162 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (160 bp):
CTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACACCAGAAA
ATGGTAGAATCAACCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAATA
CAATATGTAACGCATGAAAATCAGTAACGC
Found at i:100515 original size:59 final size:59
Alignment explanation
Indices: 100352--100518 Score: 246
Period size: 59 Copynumber: 2.8 Consensus size: 59
100342 AGTACAATTT
* *
100352 GTAACGCCTGAAAATGTTAAAATCAACCAATTAATACAATCTGTAACGCATGAAAATCA
1 GTAACGCCTGAAAATGTTAGAATCAACCAACTAATACAATCTGTAACGCATGAAAATCA
* *
100411 GTAACGCCTGAAAATGTTAGAATCAACACATC-AATACAATCTGTAACGTATGAAAATCA
1 GTAACGCCTGAAAATGTTAGAATCAAC-CAACTAATACAATCTGTAACGCATGAAAATCA
* * * *
100470 GTAACGCCTGAAAATGGTAGAATCAACCAACTAGTATAATTTGTAACGC
1 GTAACGCCTGAAAATGTTAGAATCAACCAACTAATACAATCTGTAACGC
100519 TTGAGAATGT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 3 0.03
59 91 0.95
60 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (59 bp):
GTAACGCCTGAAAATGTTAGAATCAACCAACTAATACAATCTGTAACGCATGAAAATCA
Found at i:100528 original size:101 final size:101
Alignment explanation
Indices: 100411--100728 Score: 386
Period size: 101 Copynumber: 3.1 Consensus size: 101
100401 ATGAAAATCA
*
100411 GTAACGCCTGAAAATGTTAGAATCAA-CACATCAATACAATCTGTAACGTATGAAAATCAGTAAC
1 GTAACGCCTGAAAATGTTAGAATCAACCA-ATCAATACAATCTGTAACGCATGAAAATCAGTAAC
* * *
100475 GCCTGAAAATGGTAGAATCAACCAACTAGTATAATTT
65 GCCTGAAAATGCTAGAATCAACCAACCAGTACAATTT
* * * * *
100512 GTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAATATGTAACGCATGAAAATCAGTAACG
1 GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
* *
100577 CCTGAAAATGCTAGAATCAGCCAACCCGTACAATTT
66 CCTGAAAATGCTAGAATCAACCAACCAGTACAATTT
** * * * * * *
100613 GTTGCGCCTAAAAATGTTAAAATCAACCAATAAATACAATCTGTAACACATGAAAATTAGTAATG
1 GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
* * * * *
100678 CCTAAAAATGTTAGAATCAACCAATCAATACAATCT
66 CCTGAAAATGCTAGAATCAACCAACCAGTACAATTT
* *
100714 GTAACACATGAAAAT
1 GTAACGCCTGAAAAT
100729 CAATGACGCC
Statistics
Matches: 180, Mismatches: 36, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
101 178 0.99
102 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (101 bp):
GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
CCTGAAAATGCTAGAATCAACCAACCAGTACAATTT
Found at i:100710 original size:59 final size:59
Alignment explanation
Indices: 100617--100753 Score: 220
Period size: 59 Copynumber: 2.3 Consensus size: 59
100607 CAATTTGTTG
* * *
100617 CGCCTAAAAATGTTAAAATCAACCAATAAATACAATCTGTAACACATGAAAATTAGTAA
1 CGCCTAAAAATGTTAGAATCAACCAATAAATACAATCTGTAACACATGAAAATCAATAA
* * *
100676 TGCCTAAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAATGA
1 CGCCTAAAAATGTTAGAATCAACCAATAAATACAATCTGTAACACATGAAAATCAATAA
100735 CGCCTAAAAATGTTAGAAT
1 CGCCTAAAAATGTTAGAAT
100754 TAGCCAACTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (59 bp):
CGCCTAAAAATGTTAGAATCAACCAATAAATACAATCTGTAACACATGAAAATCAATAA
Found at i:100896 original size:42 final size:42
Alignment explanation
Indices: 100836--100934 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
100826 ATGAATATCA
* * * * *
100836 GTAACGCCTGAAATTGTTAGAATCAGCCAACCAGTACAATTT
1 GTAACGCCTGAAAATGTTAAAATCAACCAACCAATACAATCT
*
100878 GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCT
1 GTAACGCCTGAAAATGTTAAAATCAACCAACCAATACAATCT
*
100920 GTAACGCATGAAAAT
1 GTAACGCCTGAAAAT
100935 CAGTAACGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (42 bp):
GTAACGCCTGAAAATGTTAAAATCAACCAACCAATACAATCT
Found at i:100960 original size:101 final size:100
Alignment explanation
Indices: 100667--100993 Score: 384
Period size: 101 Copynumber: 3.2 Consensus size: 100
100657 AACACATGAA
* * * *
100667 AATTAGTAATGCCTAAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAA
1 AATTTGTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAG
* * * * *
100732 TGACGCCTAAAAATGTTAGAATTAGCCAACTAGTGTAATT
66 TAACGCCT-GAAATGTTAGAATCAGCCAACCA--GT-A-C
** * * * *
100772 AATTTGTAACGTTTGAAAATGTTAGAATTAGCCAATCAATACAATTTGTAACACATGAATATCAG
1 AATTTGTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAG
100837 TAACGCCTGAAATTGTTAGAATCAGCCAACCAGTAC
66 TAACGCCTGAAA-TGTTAGAATCAGCCAACCAGTAC
* *
100873 AATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAG
1 AATTTGTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAG
* * *
100938 TAACGCCTGGAAATGTTAGAATCAACCAATCAATAC
66 TAACGCCT-GAAATGTTAGAATCAGCCAACCAGTAC
* **
100974 AATCTGTAACGTATGAAAAT
1 AATTTGTAACGCCTGAAAAT
100994 CAGTAACGCT
Statistics
Matches: 191, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
101 102 0.53
102 5 0.03
103 2 0.01
104 3 0.02
105 79 0.41
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (100 bp):
AATTTGTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACACATGAAAATCAG
TAACGCCTGAAATGTTAGAATCAGCCAACCAGTAC
Found at i:101041 original size:526 final size:527
Alignment explanation
Indices: 100049--101246 Score: 2024
Period size: 526 Copynumber: 2.3 Consensus size: 527
100039 AATACAGTGC
* *
100049 CGCCTGAAAATGTTAGAATAAGCCAACCAATAAAATTTGTAACGCCTGAAAATGTTAAAATCAAC
1 CGCCTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAAC
* * * *
100114 CAATCAATATAATCTGTAATGTATGAAAATCAGT-GTCGCCTGAAAATGTTAGAATCAACCAATC
66 CAATCAATACAATCTGTAACGCATGAAAATCAGTAAT-GCCTGAAAATGTTAGAATCAACCAATC
*
100178 AATACAATCTGTAACGCATGAAAATCAATAACGCCTAAAAATATTAGAATCAGCCAACTAGTATA
130 AATACAATCTGTAACACATGAAAATCAATAACGCCTAAAAATATTAGAATCAGCCAACTAGTATA
*
100243 ATTAATTTGTAACATCTGAAAATGTTAGAATTAGCCAATCAATACAATTCGTAACGCATGAATAT
195 ATTAATTTGTAACATCTGAAAATGTTAGAATTAGCCAATCAATACAATTCGTAACACATGAATAT
100308 CAGTAACACCAGAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAA
260 CAGTAACACCAGAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAA
*
100373 ATCAACCAATTAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGAAAATGTTAGAATCAAC
325 ATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGAAAATGTTAGAATCAAC
100438 ACATCAATACAATCTGTAACGTATGAAAATCAGTAACGCCTGAAAATGGTAGAATCAACCAACTA
390 ACATCAATACAATCTGTAACGTATGAAAATCAGTAACGCCTGAAAATGGTAGAATCAACCAACTA
100503 GTATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAATAC-AATATGTAACGCATGAAA
455 GTATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAA
100567 ATCAGTAA
520 ATCAGTAA
* ** ** *
100575 CGCCTGAAAATGCTAGAATCAGCCAACCCGTACAATTTGTTGCGCCTAAAAATGTTAAAATCAAC
1 CGCCTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAAC
* * * *
100640 CAATAAATACAATCTGTAACACATGAAAATTAGTAATGCCTAAAAATGTTAGAATCAACCAATCA
66 CAATCAATACAATCTGTAACGCATGAAAATCAGTAATGCCTGAAAATGTTAGAATCAACCAATCA
* * * *
100705 ATACAATCTGTAACACATGAAAATCAATGACGCCTAAAAATGTTAGAATTAGCCAACTAGTGTAA
131 ATACAATCTGTAACACATGAAAATCAATAACGCCTAAAAATATTAGAATCAGCCAACTAGTATAA
* * *
100770 TTAATTTGTAACGTTTGAAAATGTTAGAATTAGCCAATCAATACAATTTGTAACACATGAATATC
196 TTAATTTGTAACATCTGAAAATGTTAGAATTAGCCAATCAATACAATTCGTAACACATGAATATC
* * * *
100835 AGTAACGCCTGAAATTGTTAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAA
261 AGTAACACCAGAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAA
*
100900 TCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGGAAATGTTAGAATCAAC-
326 TCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGAAAATGTTAGAATCAACA
* * *
100964 CAATCAATACAATCTGTAACGTATGAAAATCAGTAACGCTTGAAAATGTTATAATCAACCAACTA
391 C-ATCAATACAATCTGTAACGTATGAAAATCAGTAACGCCTGAAAATGGTAGAATCAACCAACTA
101029 GTATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAA
455 GTATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAA
101094 ATCAGTAA
520 ATCAGTAA
*
101102 CGCTTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAAC
1 CGCCTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAAC
* *
101167 CAATCAATACAATCTATAACGCATGAAAATCAGTAACGCCTGAAAATGTTAGAATCAACCAATCA
66 CAATCAATACAATCTGTAACGCATGAAAATCAGTAATGCCTGAAAATGTTAGAATCAACCAATCA
101232 ATACAATCTGTAACA
131 ATACAATCTGTAACA
101247 AGAGCTGTTC
Statistics
Matches: 622, Mismatches: 47, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
525 1 0.00
526 462 0.74
527 159 0.26
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (527 bp):
CGCCTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAATGTTAAAATCAAC
CAATCAATACAATCTGTAACGCATGAAAATCAGTAATGCCTGAAAATGTTAGAATCAACCAATCA
ATACAATCTGTAACACATGAAAATCAATAACGCCTAAAAATATTAGAATCAGCCAACTAGTATAA
TTAATTTGTAACATCTGAAAATGTTAGAATTAGCCAATCAATACAATTCGTAACACATGAATATC
AGTAACACCAGAAACTGTCAGAATCAGCCAACCAGTACAATTTGTAACGCCTGAAAATGTTAAAA
TCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACGCCTGAAAATGTTAGAATCAACA
CATCAATACAATCTGTAACGTATGAAAATCAGTAACGCCTGAAAATGGTAGAATCAACCAACTAG
TATAATTTGTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAAA
TCAGTAA
Found at i:101043 original size:59 final size:59
Alignment explanation
Indices: 100878--101025 Score: 251
Period size: 59 Copynumber: 2.5 Consensus size: 59
100868 AGTACAATTT
100878 GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCA
1 GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCA
* * *
100937 GTAACGCCTGGAAATGTTAGAATCAACCAATCAATACAATCTGTAACGTATGAAAATCA
1 GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCA
* *
100996 GTAACGCTTGAAAATGTTATAATCAACCAA
1 GTAACGCCTGAAAATGTTAAAATCAACCAA
101026 CTAGTATAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 83 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (59 bp):
GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCA
Found at i:101112 original size:102 final size:101
Alignment explanation
Indices: 100937--101245 Score: 456
Period size: 101 Copynumber: 3.0 Consensus size: 101
100927 ATGAAAATCA
* *
100937 GTAACGCCTGGAAATGTTAGAATCAACCAATCAATACAATCTGTAACGTATGAAAATCAGTAACG
1 GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
* * * *
101002 CTTGAAAATGTTATAATCAACCAACTAGTATAATTT
66 CTTGAAAATGTTAGAATCAACCAACCAATACAATTT
* * * * *
101038 GTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAAATCAGTAAC
1 GTAACGCCTGAAAATGTTAGAATCAACCAATCAATAC-AATCTGTAACGCATGAAAATCAGTAAC
*
101103 GCTTGAAAATGTTAGAATCAGCCAACCAATACAATTT
65 GCTTGAAAATGTTAGAATCAACCAACCAATACAATTT
* *
101140 GTAACGCCTGAAAATGTTAAAATCAACCAATCAATACAATCTATAACGCATGAAAATCAGTAACG
1 GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
* * *
101205 CCTGAAAATGTTAGAATCAACCAATCAATACAATCT
66 CTTGAAAATGTTAGAATCAACCAACCAATACAATTT
101241 GTAAC
1 GTAAC
101246 AAGAGCTGTT
Statistics
Matches: 184, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
101 95 0.52
102 89 0.48
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (101 bp):
GTAACGCCTGAAAATGTTAGAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAACG
CTTGAAAATGTTAGAATCAACCAACCAATACAATTT
Found at i:101133 original size:60 final size:59
Alignment explanation
Indices: 101038--101154 Score: 180
Period size: 60 Copynumber: 2.0 Consensus size: 59
101028 AGTATAATTT
* * *
101038 GTAACGCTTGAGAATGTTAGAATTAGCCAATCAATACAAATATGTAACGCATGAAAATCA
1 GTAACGCTTGAAAATGTTAGAATCAGCCAACCAATAC-AATATGTAACGCATGAAAATCA
* *
101098 GTAACGCTTGAAAATGTTAGAATCAGCCAACCAATACAATTTGTAACGCCTGAAAAT
1 GTAACGCTTGAAAATGTTAGAATCAGCCAACCAATACAATATGTAACGCATGAAAAT
101155 GTTAAAATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
59 18 0.35
60 34 0.65
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (59 bp):
GTAACGCTTGAAAATGTTAGAATCAGCCAACCAATACAATATGTAACGCATGAAAATCA
Found at i:101157 original size:42 final size:42
Alignment explanation
Indices: 101093--101196 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
101083 AACGCATGAA
* * * *
101093 AATCAGTAACGCTTGAAAATGTTAGAATCAGCCAACCAATAC
1 AATCTGTAACGCATGAAAATGTTAAAATCAACCAACCAATAC
* * *
101135 AATTTGTAACGCCTGAAAATGTTAAAATCAACCAATCAATAC
1 AATCTGTAACGCATGAAAATGTTAAAATCAACCAACCAATAC
*
101177 AATCTATAACGCATGAAAAT
1 AATCTGTAACGCATGAAAAT
101197 CAGTAACGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (42 bp):
AATCTGTAACGCATGAAAATGTTAAAATCAACCAACCAATAC
Found at i:102041 original size:17 final size:17
Alignment explanation
Indices: 102021--102057 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
102011 CAATCAATAC
*
102021 AATCTGTAACGCATGAA
1 AATCAGTAACGCATGAA
*
102038 AATCAGTAACGCCTGAA
1 AATCAGTAACGCATGAA
102055 AAT
1 AAT
102058 GTTAGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (17 bp):
AATCAGTAACGCATGAA
Found at i:102060 original size:59 final size:59
Alignment explanation
Indices: 101988--102125 Score: 249
Period size: 59 Copynumber: 2.3 Consensus size: 59
101978 AAACCAGTCT
* * *
101988 CGCCTAAAAATGTTAAAATCAACCAATCAATACAATCTGTAACGCATGAAAATCAGTAA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATATGTAACGCATGAAAATCAGTAA
102047 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATATGTAACGCATGAAAATCAGTAA
1 CGCCTGAAAATGTTAGAATCAACCAATCAATACAATATGTAACGCATGAAAATCAGTAA
102106 CGCCTGAAAATGTTAGAATC
1 CGCCTGAAAATGTTAGAATC
102126 GGCCAACTAG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 76 1.00
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (59 bp):
CGCCTGAAAATGTTAGAATCAACCAATCAATACAATATGTAACGCATGAAAATCAGTAA
Done.