Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019875.1 Corchorus olitorius cultivar O-4 contig19908, 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: 103585
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:959 original size:22 final size:22
Alignment explanation
Indices: 933--977 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
923 ACTAAAATGG
* *
933 GACTTT-TCAACATAAAGTAAAA
1 GACTTTATAAACA-AAAATAAAA
955 GACTTTATAAACAAAAATAAAA
1 GACTTTATAAACAAAAATAAAA
977 G
1 G
978 GTTTTAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (22 bp):
GACTTTATAAACAAAAATAAAA
Found at i:9164 original size:35 final size:39
Alignment explanation
Indices: 9118--9188 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 39
9108 TATATTATTA
*
9118 TTAATAATATTA-ATAT-ATATA-TATA-GTATTTTCCG
1 TTAAAAATATTATATATCATATATTATATGTATTTTCCG
9153 TTAAAAATATTATATATCATATATTATATGTATTTT
1 TTAAAAATATTATATATCATATATTATATGTATTTT
9189 ATATATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 11 0.35
36 4 0.13
37 5 0.16
38 4 0.13
39 7 0.23
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (39 bp):
TTAAAAATATTATATATCATATATTATATGTATTTTCCG
Found at i:9358 original size:23 final size:22
Alignment explanation
Indices: 9306--9347 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
9296 TAGATTAGTT
9306 TTCA-TCTCTTCTTTCTCTCTC
1 TTCACTCTCTTCTTTCTCTCTC
9327 TTCACTCTCGTTCTTTCTCTC
1 TTCACTCTC-TTCTTTCTCTC
9348 ATTTCTGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.05, C:0.38, G:0.02, T:0.55
Consensus pattern (22 bp):
TTCACTCTCTTCTTTCTCTCTC
Found at i:13575 original size:24 final size:25
Alignment explanation
Indices: 13522--13575 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
13512 ATTAGCTAGT
*
13522 CATAATTATAATAAAAACACAAGAA
1 CATAATTATAATAAAAAAACAAGAA
* *
13547 AATAATT-TATTAAAAAAACATA-AA
1 CATAATTATAATAAAAAAACA-AGAA
13571 CATAA
1 CATAA
13576 AAGAGAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (25 bp):
CATAATTATAATAAAAAAACAAGAA
Found at i:15060 original size:10 final size:11
Alignment explanation
Indices: 15035--15065 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
15025 TGTAAAAAGT
15035 GTGGTTAAAAA
1 GTGGTTAAAAA
15046 GTGGTTAAAAA
1 GTGGTTAAAAA
15057 -TGGTTAAAA
1 GTGGTTAAAA
15066 GTGTGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (11 bp):
GTGGTTAAAAA
Found at i:15229 original size:16 final size:16
Alignment explanation
Indices: 15208--15239 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15198 AGGAATAAGC
15208 AATCAAGCAAAGCAAT
1 AATCAAGCAAAGCAAT
15224 AATCAAGCAAAGCAAT
1 AATCAAGCAAAGCAAT
15240 GCAAAGAAAA
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:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
AATCAAGCAAAGCAAT
Found at i:22809 original size:25 final size:25
Alignment explanation
Indices: 22780--22827 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
22770 TAACGAATTT
22780 CATTTGAGAAAATCGTCTTCCAACA
1 CATTTGAGAAAATCGTCTTCCAACA
* * *
22805 CATTTGAGGAGATTGTCTTCCAA
1 CATTTGAGAAAATCGTCTTCCAA
22828 TCAATTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (25 bp):
CATTTGAGAAAATCGTCTTCCAACA
Found at i:22948 original size:40 final size:39
Alignment explanation
Indices: 22839--22950 Score: 95
Period size: 40 Copynumber: 2.8 Consensus size: 39
22829 CAATTTCTAA
* *
22839 TTCTGAAAATCT-TTCTGAAA-AATCGTCTTCCGATTGGC
1 TTCTGAAAATCTATTCT-AAATAACCGTCTTCCGATTGAC
* * * * * *
22877 TTCTGAATATTTAAATCT-GATAAACCTTCTTCTGATTGAC
1 TTCTGAAAATCT-ATTCTAAAT-AACCGTCTTCCGATTGAC
22917 TTCTGAAAATCTACTTCTAAATAACCGTCTTCCG
1 TTCTGAAAATCTA-TTCTAAATAACCGTCTTCCG
22951 GTGCATCTCT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
38 11 0.20
39 1 0.02
40 40 0.74
41 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (39 bp):
TTCTGAAAATCTATTCTAAATAACCGTCTTCCGATTGAC
Found at i:23096 original size:64 final size:64
Alignment explanation
Indices: 22958--23345 Score: 551
Period size: 64 Copynumber: 6.0 Consensus size: 64
22948 CCGGTGCATC
* * * * *
22958 TCTTAACAAGATCATCTTCCGATCAACTTCTGAAACCTTTTCGAGAAACTATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACT
* * * * * *
23023 TTTTAACAAGATCGTCTTTCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
23087 TCTTGACAAGATCGTCTTCCGATCAACTTTTGAAAACTCTTAAGAAACCAACTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
23151 TCTTGATAAGTTCGTCTTCCGATAAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * *
23215 TCTTGACAATATCGTTTTCCGATCAACTCCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* * * *
23279 TCTTGACAAGATCGTCTTCTGATCAACTTCTGAAAATTGTTGAGAAACAATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
23343 TCT
1 TCT
23346 AAAATCCTCT
Statistics
Matches: 288, Mismatches: 35, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
64 252 0.88
65 36 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:26172 original size:14 final size:13
Alignment explanation
Indices: 26143--26184 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
26133 TAAAAGACTC
26143 AAAACC-TTTTTG
1 AAAACCTTTTTTG
26155 -AAACCTATTTTTG
1 AAAACCT-TTTTTG
26168 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
26182 AAA
1 AAA
26185 GCAATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:27268 original size:19 final size:18
Alignment explanation
Indices: 27244--27279 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27234 TGAAGACTTA
27244 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
27263 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
27280 ATTATCTCAA
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:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:38100 original size:47 final size:47
Alignment explanation
Indices: 38046--38978 Score: 1308
Period size: 47 Copynumber: 19.7 Consensus size: 47
38036 AATAGAGGCT
*
38046 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATG
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * *
38093 AGTTTAATTTTAGGTAATTATACTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
38140 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGTGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38187 AGTTTAATTCTAGGTAATTAAACAAAATAGTAAAAGAAGAAAAGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
38234 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATG
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38281 AGTTTAATTCTAGGTAATTAAACTATATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38328 AGTTTAATTATAGGTTATTAAACTAAATAGTAAAAGAAGAAGTA-ATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAG-AGATC
* *
38375 AGTTTAATTCTAGGTAATTAAACTAAAGAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
38422 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
38469 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
38516 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38563 AGATTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * * *
38610 ACTTTAATTCTAGGTGATTAAAC-AACATAGTAAAAGAAGAAGAAATT
1 AGTTTAATTCTAGGTAATTAAACTAA-ATAGTAAAAGAAGAAGAGATC
* *
38657 AGTTTACTTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38704 AGTTTAATTCTAGGTAATTAATCTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
38751 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAG-AGAAGGTT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAG-AGATC
* * *
38798 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAAAAGATG-TT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGA-GATC
* * * *
38845 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAAAGGAAGTAAACAGTAAC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGT--AAAA-GAAG--AAGAG-ATC
** * *
38898 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAG-A-AAGAGTAAAC
1 -AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAG--ATC
*
38946 AG--TAATTCT-GAGTAATTAAACTAAAAAGTAAAA
1 AGTTTAATTCTAG-GTAATTAAACTAAATAGTAAAA
38979 AGTAGTAATA
Statistics
Matches: 812, Mismatches: 57, Indels: 36
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.00
45 27 0.03
46 5 0.01
47 723 0.89
48 9 0.01
49 4 0.00
50 4 0.00
51 2 0.00
52 7 0.01
54 30 0.04
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (47 bp):
AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
Found at i:38945 original size:54 final size:54
Alignment explanation
Indices: 38844--38950 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
38834 AAAAAGATGT
* *
38844 TAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAAAGGAAGTAAACAGTAAC
1 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGTAAC
38898 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAGAAAG-AGTAAACAGTAA
1 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAA-AAAGAAGTAAACAGTAA
38951 TTCTGAGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.25
Consensus pattern (54 bp):
TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGTAAC
Found at i:43910 original size:41 final size:41
Alignment explanation
Indices: 43851--44066 Score: 201
Period size: 41 Copynumber: 5.3 Consensus size: 41
43841 ACATTTTAGC
* * * *
43851 AGCCCCGAGCAGGCTTTTCAGTAGTCGAGTAGATTTCCAAT
1 AGCCCCGAGCAGACTTTTCAGTATTCAAGTAGATTTCCAGT
* *
43892 AACCCCGAGCAAACTTTTCAGTACTT-AAGTAGATTTCCAGT
1 AGCCCCGAGCAGACTTTTCAGTA-TTCAAGTAGATTTCCAGT
* *
43933 AGCCCCGAGCGGGCTTTTCAGTATTCATA-TAGATTTCCAGT
1 AGCCCCGAGCAGACTTTTCAGTATTCA-AGTAGATTTCCAGT
* * *
43974 AGCCCCGAGCAGACCTTTCCGTATTCAAGTAGAGTTCCAGT
1 AGCCCCGAGCAGACTTTTCAGTATTCAAGTAGATTTCCAGT
** *
44015 -GCCCTAAGCAGGTATCTTTT-A-TATTTAAGTAGATTT-CAGT
1 AGCCCCGAGCA-G-A-CTTTTCAGTATTCAAGTAGATTTCCAGT
* *
44055 AACCCTGAGCAG
1 AGCCCCGAGCAG
44067 GCCTTTTAGC
Statistics
Matches: 144, Mismatches: 23, Indels: 17
0.78 0.12 0.09
Matches are distributed among these distances:
40 16 0.11
41 121 0.84
42 3 0.02
43 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (41 bp):
AGCCCCGAGCAGACTTTTCAGTATTCAAGTAGATTTCCAGT
Found at i:48028 original size:47 final size:47
Alignment explanation
Indices: 47959--49038 Score: 1439
Period size: 47 Copynumber: 22.7 Consensus size: 47
47949 TACAATCGAA
* * * * * * *
47959 AGTTTAAATC-AGAGTAATTAAACTAAAGAGCAAGAGAAAAAGAAAAC
1 AGTTTAATTCTAG-GTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * *
48006 AGTTTAATTCTTGGTAATTAAACAAAAGAGTAAAAGTAAAAGTAAACTGAGA-C
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAG---AAG--AA--GAGATC
*
48059 TAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATG
1 -AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
48107 AGTTTAATTCTAGGTAATTATACTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48154 AGTTTAATTCTAGGAAATTAAACTAAATAGTAAAAGAAGAAGAGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48201 AGTTTAATTCTAGGTAATTAAACTAAATTGTAAAAGAAGAAGAGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
48248 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGATATG
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48295 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48342 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGGTC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48389 AGTTTAATTCTAGATAATTAAACTAAATAGTAAAAGAAGAAGAGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * *
48436 AGTTTAATTCTAGATAATTAAACAAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* *
48483 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAACAAGAAGAGATG
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
48530 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48577 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * * *
48624 AGTTTAATTCTAGGTAATCAAA-TAAATAGGAAAAGAAGAAGAGTTT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
*
48670 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
* * *
48717 AGTTTACTTCTAGGTAATTAAACTAAATAGTAAAAGAATAAGAGATT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
48764 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGATG-TC
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGA-GATC
* *
48811 AATTTAATTCTAGGTAATTAAACTAAATAGTAAAAGTAGAGAAG-G-TT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAG-A-AGAAGAGATC
* *
48858 AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGATG-TT
1 AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGA-GATC
* * *
48905 AGTTTAATTCTGGGTAATTAAACTAAAGT-GTAAAAAAGGAAGTAAACAGTAAC
1 AGTTTAATTCTAGGTAATTAAACTAAA-TAGT--AAAA-GAAG--AAGAG-ATC
** * *
48958 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAG-A-AAGAGTAAAC
1 -AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAG--ATC
*
49006 AG--TAATTCT-GAGTAATTAAACTAAAAAGTAAAA
1 AGTTTAATTCTAG-GTAATTAAACTAAATAGTAAAA
49039 AGTAGTAATA
Statistics
Matches: 945, Mismatches: 60, Indels: 58
0.89 0.06 0.05
Matches are distributed among these distances:
44 1 0.00
45 32 0.03
46 44 0.05
47 764 0.81
48 7 0.01
49 11 0.01
50 7 0.01
51 5 0.01
52 9 0.01
53 1 0.00
54 64 0.07
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (47 bp):
AGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAGAGATC
Found at i:49006 original size:54 final size:54
Alignment explanation
Indices: 48857--49010 Score: 180
Period size: 54 Copynumber: 3.0 Consensus size: 54
48847 TAGAGAAGGT
* * * *
48857 TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAG---A-TGT---
1 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGTAAC
* * *
48904 TAGTTTAATTCTGGGTAATTAAACTAAAGTGTAAAAAAGGAAGTAAACAGTAAC
1 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGTAAC
48958 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAGAAAG-AGTAAACAGTAA
1 TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAA-AAAGAAGTAAACAGTAA
49011 TTCTGAGTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
47 39 0.43
50 1 0.01
51 2 0.02
54 46 0.51
55 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (54 bp):
TAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAAAAGAAGTAAACAGTAAC
Found at i:66494 original size:21 final size:21
Alignment explanation
Indices: 66468--66516 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
66458 TTTAAATTCG
66468 CATTGGAGAAGATTCCAAGCT
1 CATTGGAGAAGATTCCAAGCT
* *
66489 CATTGGAGAAGGTTTCAAGCT
1 CATTGGAGAAGATTCCAAGCT
66510 CATTGGA
1 CATTGGA
66517 ATTGCCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
CATTGGAGAAGATTCCAAGCT
Found at i:67476 original size:18 final size:18
Alignment explanation
Indices: 67453--67489 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
67443 TAGGAGTTCA
67453 TTGGAGAAGGTTCCAAGC
1 TTGGAGAAGGTTCCAAGC
*
67471 TTGGAGAAGGTTTCAAGC
1 TTGGAGAAGGTTCCAAGC
67489 T
1 T
67490 CATTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (18 bp):
TTGGAGAAGGTTCCAAGC
Found at i:72618 original size:17 final size:17
Alignment explanation
Indices: 72596--72628 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
72586 GTGTGTTTGC
72596 AGCCCCTCCACTTGCAA
1 AGCCCCTCCACTTGCAA
72613 AGCCCCTCCACTTGCA
1 AGCCCCTCCACTTGCA
72629 GAGTCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.48, G:0.12, T:0.18
Consensus pattern (17 bp):
AGCCCCTCCACTTGCAA
Found at i:75570 original size:76 final size:76
Alignment explanation
Indices: 75419--75563 Score: 168
Period size: 76 Copynumber: 1.9 Consensus size: 76
75409 ACAAGGACCT
** * *
75419 CGACTCCACCTGGGCGCCCACATGGTTGCCTTTAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
75484 GGGCAATGTCA
66 GGGCAATGTCA
** * * **
75495 CGACTCCAGTTGGGTGCCCACATGGTTTGTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTGAAGCACCCATGTGGTTT-GCCTGAGAACCCAG
75558 ATGGGC
64 ATGGGC
75564 TGTGTCATAG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
75 4 0.07
76 46 0.81
77 7 0.12
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAATGTCA
Found at i:85792 original size:17 final size:17
Alignment explanation
Indices: 85770--85816 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
85760 TTTAATTCTC
85770 TGCTTTTATAATTCAAT
1 TGCTTTTATAATTCAAT
* *
85787 TGCTTTTAGT-TTTTAAT
1 TGCTTTTA-TAATTCAAT
*
85804 TGTTTTTATAATT
1 TGCTTTTATAATT
85817 TCTCTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.62
Consensus pattern (17 bp):
TGCTTTTATAATTCAAT
Found at i:97777 original size:109 final size:109
Alignment explanation
Indices: 97586--97906 Score: 534
Period size: 109 Copynumber: 2.9 Consensus size: 109
97576 CCTCAGTTTT
* * *
97586 ACTATATATGGCGGCGTTTGAGGTGTAAAACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
1 ACTATATATGGCGGCGTCTGAGCTGTAAGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
97651 CCGCCATGTATAGTAAAATTGAGGAAACTTCCTGGGTCAATTTC
66 CCGCCATGTATAGTAAAATTGAGGAAACTTCCTGGGTCAATTTC
*
97695 ACTATATATGGCGGCGTCTGAGCTGTTAGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
1 ACTATATATGGCGGCGTCTGAGCTGTAAGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
*
97760 CCGCCATGTATAGTAAAATTTAGGAAACTTCCTGGGTCAATTTC
66 CCGCCATGTATAGTAAAATTGAGGAAACTTCCTGGGTCAATTTC
* * *
97804 ACTATATATGGCGGCGTCTAAGCTGTGAGACGCCGCTATTTTAGTGGCGTTTCAAAGCTCAGACG
1 ACTATATATGGCGGCGTCTGAGCTGTAAGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
* * *
97869 CCGCCATATATAGTGAAATCGAGGAAACTTCCTCGGGT
66 CCGCCATGTATAGTAAAATTGAGGAAACTTCCT-GGGT
97907 TGCCTTCATT
Statistics
Matches: 199, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
109 195 0.98
110 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (109 bp):
ACTATATATGGCGGCGTCTGAGCTGTAAGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACG
CCGCCATGTATAGTAAAATTGAGGAAACTTCCTGGGTCAATTTC
Found at i:99139 original size:2 final size:2
Alignment explanation
Indices: 99132--99159 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99122 TTTCATGTTA
99132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99160 TACCTTGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101854 original size:22 final size:22
Alignment explanation
Indices: 101829--101876 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
101819 TGTTAATTAG
101829 TTTAAAGCAGATCTGATCTTGA
1 TTTAAAGCAGATCTGATCTTGA
101851 TTTAAAGCAGATCTGATCTTGA
1 TTTAAAGCAGATCTGATCTTGA
101873 TTTA
1 TTTA
101877 CAGTTCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTAAAGCAGATCTGATCTTGA
Found at i:103169 original size:16 final size:16
Alignment explanation
Indices: 103115--103183 Score: 79
Period size: 16 Copynumber: 4.2 Consensus size: 16
103105 ATTAATTTGA
103115 TCTTGACATCTTTGTT
1 TCTTGACATCTTTGTT
* *
103131 TCTT-CCATTCAATTTG-A
1 TCTTGACA-TC--TTTGTT
103148 TCTTGACATCTTTGTT
1 TCTTGACATCTTTGTT
103164 TCTTGACATCTTTGTT
1 TCTTGACATCTTTGTT
103180 TCTT
1 TCTT
103184 CCATTCAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 6 0.14
16 26 0.59
17 6 0.14
18 6 0.14
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.55
Consensus pattern (16 bp):
TCTTGACATCTTTGTT
Done.