Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1494
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: 26039
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Found at i:1939 original size:18 final size:18
Alignment explanation
Indices: 1894--1939 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
1884 TTTGTCTATT
1894 TATAATTACA-TATTTTTA
1 TATAATTA-ATTATTTTTA
*
1912 TAT-A-TGATTATTTTTA
1 TATAATTAATTATTTTTA
1928 TATAATTAATTA
1 TATAATTAATTA
1940 CTAAATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 2 0.09
18 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TATAATTAATTATTTTTA
Found at i:2507 original size:2 final size:2
Alignment explanation
Indices: 2500--2540 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2490 ACATAGCCTG
2500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2541 ATCAACGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3246 original size:16 final size:15
Alignment explanation
Indices: 3223--3284 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
3213 TATAAAAATT
3223 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
3238 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* *
3253 TTTATTTAAA-AATA
1 TTTAATTAAATAAAA
3267 TTTAA-TAAAT-AAA
1 TTTAATTAAATAAAA
3280 TTTAA
1 TTTAA
3285 CATTAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.28
14 11 0.28
15 13 0.32
16 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:3308 original size:44 final size:45
Alignment explanation
Indices: 3212--3296 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
3202 GTTTTAATAT
* *
3212 TTATAAAAATTTTTAATTAAATAAAATTATAATTAATAAAATTTA
1 TTATAAAAATATTTAATTAAATAAAATTATAATCAATAAAATTTA
*
3257 TT-TAAAAATATTTAA-TAAAT-AAATT-TAA-CATTAAAATTTA
1 TTATAAAAATATTTAATTAAATAAAATTATAATCAATAAAATTTA
3297 ATCATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 10 0.27
41 3 0.08
42 5 0.14
43 5 0.14
44 12 0.32
45 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (45 bp):
TTATAAAAATATTTAATTAAATAAAATTATAATCAATAAAATTTA
Found at i:8756 original size:69 final size:70
Alignment explanation
Indices: 8668--8817 Score: 232
Period size: 69 Copynumber: 2.2 Consensus size: 70
8658 GGAATGGGGA
*
8668 TGGAGTAT-CCTCGATAATGATAATTTGGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAAC
1 TGGAGTATCCCTCGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAAC
8732 AGGGT
66 AGGGT
* * * *
8737 TGGAGTATCCCT-GACAATGATAATTTGGATAAAATAAGATTTAAATTTTGATGAGTTTAAAAAT
1 TGGAGTATCCCTCGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAAC
*
8801 GGGGT
66 AGGGT
8806 TGGAGTATCCCT
1 TGGAGTATCCCT
8818 TCGGAGGAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
69 71 0.96
70 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (70 bp):
TGGAGTATCCCTCGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAAC
AGGGT
Found at i:9052 original size:97 final size:97
Alignment explanation
Indices: 8733--9043 Score: 410
Period size: 97 Copynumber: 3.2 Consensus size: 97
8723 TTTAAAAACA
* * * * * *
8733 GGGTTGGAGTATCCCTGACAATGATAATTTGGA--TAAAATAAGATTTAAATTTTGATGAGTTTA
1 GGGTTGGAGTATCCCCGATAATGACAATTT-AACCAAAAATAAGATTTAAATTTTGATAAGTTTA
8796 AAAATGGGGTTGGAGTATCCCTTCGGAGGAATG
65 AAAATGGGGTTGGAGTATCCCTTCGGAGGAATG
*
8829 GGGTTGGAGTATCCCCGATAATGACAATTTAACCAAAAATAAGATTTAAATTTTGATAAATTTAA
1 GGGTTGGAGTATCCCCGATAATGACAATTTAACCAAAAATAAGATTTAAATTTTGATAAGTTTAA
* * *
8894 AAATGGGGTTAGAGCATCCCTTTGGAGGAATG
66 AAATGGGGTTGGAGTATCCCTTCGGAGGAATG
* * * * *
8926 GGTTTGGAGTGTCCTCAATTATGACAATTTAACCAAAAATAAGATTTAAATTTTGATAAGTTTAA
1 GGGTTGGAGTATCCCCGATAATGACAATTTAACCAAAAATAAGATTTAAATTTTGATAAGTTTAA
** * * *
8991 AAGCGAGGTTGGAGTATCCCCTCGGAAGAATG
66 AAATGGGGTTGGAGTATCCCTTCGGAGGAATG
*
9023 GGGTTGGTGTATCCCCGATAA
1 GGGTTGGAGTATCCCCGATAA
9044 ACAAAATTTT
Statistics
Matches: 183, Mismatches: 30, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
95 1 0.01
96 27 0.15
97 155 0.85
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (97 bp):
GGGTTGGAGTATCCCCGATAATGACAATTTAACCAAAAATAAGATTTAAATTTTGATAAGTTTAA
AAATGGGGTTGGAGTATCCCTTCGGAGGAATG
Found at i:10069 original size:14 final size:15
Alignment explanation
Indices: 10045--10073 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10035 ATCAACATAG
10045 AATGAAGAAAGAAAA
1 AATGAAGAAAGAAAA
10060 AATG-AGAAAGAAAA
1 AATGAAGAAAGAAAA
10074 CATGCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
AATGAAGAAAGAAAA
Found at i:10825 original size:26 final size:27
Alignment explanation
Indices: 10777--10833 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
10767 TGTTCACCAG
* *
10777 CAGCTTGCTGTCTTCTTCCTTCTCCAT
1 CAGCTTGCTGTCTTCTTCATTCTCCAC
* *
10804 CAGC-TGCTGTCTTTTTTATTCTCCAC
1 CAGCTTGCTGTCTTCTTCATTCTCCAC
10830 CAGC
1 CAGC
10834 AGTTGCTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.11, C:0.35, G:0.12, T:0.42
Consensus pattern (27 bp):
CAGCTTGCTGTCTTCTTCATTCTCCAC
Found at i:11420 original size:27 final size:27
Alignment explanation
Indices: 11388--11449 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
11378 AAATTTTTTA
* * *
11388 TTTTGATTTGA-TGATTTTTTTTACTT
1 TTTTGATTTCATTGATTTTTTTGAATT
11414 TGTTTGA-TTCATTGATTTTTTTGAATT
1 T-TTTGATTTCATTGATTTTTTTGAATT
11441 TTTTGATTT
1 TTTTGATTT
11450 TTGATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (27 bp):
TTTTGATTTCATTGATTTTTTTGAATT
Found at i:15513 original size:166 final size:165
Alignment explanation
Indices: 15264--15845 Score: 486
Period size: 166 Copynumber: 3.5 Consensus size: 165
15254 GTAGGAAACT
* * * * *
15264 AAAAAAAATAAAAATTCATG-AAATAAATTGAAATTTTTAAAACTAATTTAAT-TGGAGCTT-AA
1 AAAAAAATTAAAAACTCATGAAAATGAA-TGAATTTTTTAAAACTAATTTAATAT-GA-ATTAAA
* * ** * * *
15326 TAAAAATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAACCCCCTCAAAAATATTTATAAA
63 TAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAA-TCCCTCAAAAATATTTACAAA
* * ***
15391 AT-AGAAAACTTG-ATTTTTTAAA-AATAGAAAAATTTCAA-
127 ATAAAAAAACTTGTATCTCGGAAACAA-A-AAAAA-TTCAAG
* *
15429 AGAAAAAATTTAAAACTCATGAAAATGAATGAATTTTTTAAAAATAATTTAATATGAATTAAATA
1 A-AAAAAATTAAAAACTCATGAAAATGAATGAATTTTTTAAAACTAATTTAATATGAATTAAATA
* * * * *
15494 ATAATATTTGATAAATTTTAAAAATTAAAAATCAAGAAAAATCCCTCCAATAACATTTACAGAAT
65 ATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCT-CAAAAATATTTACAAAAT
*
15559 AAAAAAATTTGTATCTCGGAAACAAAAAAAATTCAAG
129 AAAAAAACTTGTATCTCGGAAACAAAAAAAATTCAAG
* * * * *
15596 AAAAAAATGGAAAAACTCATGAAAATGGATAAATTTTTGAAAACTAATTTAATATAAATTAAATA
1 AAAAAAAT-TAAAAACTCATGAAAATGAATGAATTTTTTAAAACTAATTTAATATGAATTAAATA
* * **
15661 ATAATATTTTATGAATTTTACAAATTAAAAACCAAGAAAAATATCCCT-AAAAATATTTACGGAA
65 ATAATATTTGATGAATTTTAAAAATTAAAAACCAAG-AAAA-ATCCCTCAAAAATATTTACAAAA
** * * * **
15725 TAAAAAATTTTGTATTTTGCAAACAAAAGGAATTCCAA-
128 TAAAAAAACTTGTATCTCGGAAACAAAAAAAATT-CAAG
* * * * * * * * *
15763 AAGAAAATCAATAACTTAT-AAAATAAAAGTAATTTTTCAAAATTGATTTAATGATG-ATTAAAT
1 AAAAAAATTAAAAACTCATGAAAATGAATG-AATTTTTTAAAACTAATTTAAT-ATGAATTAAAT
15826 AATAATATTTAGA-GAATTTT
64 AATAATATTT-GATGAATTTT
15846 GATGTTCAAA
Statistics
Matches: 343, Mismatches: 58, Indels: 31
0.79 0.13 0.07
Matches are distributed among these distances:
165 13 0.04
166 155 0.45
167 153 0.45
168 14 0.04
169 8 0.02
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (165 bp):
AAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTTAAAACTAATTTAATATGAATTAAATAA
TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCAAAAATATTTACAAAATAA
AAAAACTTGTATCTCGGAAACAAAAAAAATTCAAG
Found at i:15751 original size:167 final size:166
Alignment explanation
Indices: 15440--15752 Score: 448
Period size: 167 Copynumber: 1.9 Consensus size: 166
15430 GAAAAAATTT
* * *
15440 AAAACTCATGAAAATGAATGAATTTTTTAAAAATAATTTAATATGAATTAAATAATAATATTTGA
1 AAAACTCATGAAAATGAATAAATTTTTGAAAAATAATTTAATATAAATTAAATAATAATATTTGA
* *
15505 TAAATTTTAAAAATTAAAAATCAAGAAAAATCCCTCCAATAACATTTACAGAATAAAAAAATTTG
66 TAAATTTTAAAAATTAAAAACCAAGAAAAATCCCT-CAAAAACATTTACAGAATAAAAAAATTTG
*
15570 TATCTCGGAAACAAAAAAAATTCAAGAAAAAAATGGA
130 TATCTCGCAAACAAAAAAAATTCAAGAAAAAAATGGA
* * *
15607 AAAACTCATGAAAATGGATAAATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTTA
1 AAAACTCATGAAAATGAATAAATTTTTGAAAAATAATTTAATATAAATTAAATAATAATATTTGA
* * * * *
15672 TGAATTTTACAAATTAAAAACCAAGAAAAATATCCCT-AAAAATATTTACGGAATAAAAAATTTT
66 TAAATTTTAAAAATTAAAAACCAAG-AAAA-ATCCCTCAAAAACATTTACAGAATAAAAAAATTT
* *
15736 GTATTTTGCAAACAAAA
129 GTATCTCGCAAACAAAA
15753 GGAATTCCAA
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
167 118 0.92
168 4 0.03
169 6 0.05
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (166 bp):
AAAACTCATGAAAATGAATAAATTTTTGAAAAATAATTTAATATAAATTAAATAATAATATTTGA
TAAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCAAAAACATTTACAGAATAAAAAAATTTGT
ATCTCGCAAACAAAAAAAATTCAAGAAAAAAATGGA
Found at i:16873 original size:43 final size:43
Alignment explanation
Indices: 16810--17093 Score: 172
Period size: 43 Copynumber: 6.7 Consensus size: 43
16800 TGATCGAGAT
*
16810 TAAACCGATAAGTCAACAAAGGATAAAAGGATTTACTTAGGAC
1 TAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGAC
* * * * * * *
16853 TAAGCCGACAGGT-AGACAAAGGAT-AAAGCGGTTGA-TCAAGAT
1 TAAACCGACAAGTCA-ACAAAGGATAAAAG-GATTTACTTAGGAC
*
16895 TAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTGGGAC
1 TAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGAC
* ** * * * * * * * *
16938 TGAATTGATAAGTAAACAAAGAAT-ACAGCAGTTGA--TCGAGAT
1 TAAACCGACAAGTCAACAAAGGATAAAAGGA-TTTACTTAG-GAC
* *
16980 TAAACCGATAAGTCAACAAAGGATAAAAGGATTTAC-TAGGGGC
1 TAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTA-GGAC
* * * * * *
17023 TGAGCCGACAAGTAAACAAAGGATATAAAAGG-TTAACTGA-GAT
1 TAAACCGACAAGTCAACAAAGG--ATAAAAGGATTTACTTAGGAC
* *
17066 TGAACTGACAAGTCAACAAAGGATAAAA
1 TAAACCGACAAGTCAACAAAGGATAAAA
17094 AGCGATTCTT
Statistics
Matches: 179, Mismatches: 49, Indels: 28
0.70 0.19 0.11
Matches are distributed among these distances:
41 8 0.04
42 61 0.34
43 96 0.54
44 5 0.03
45 9 0.05
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.19
Consensus pattern (43 bp):
TAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGAC
Found at i:16887 original size:85 final size:85
Alignment explanation
Indices: 16798--17093 Score: 364
Period size: 85 Copynumber: 3.5 Consensus size: 85
16788 AGATACAAAA
*
16798 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTTACTTAGGACTAAGCCGACA
1 GTTGATCGAGATTAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGACTAAGCCGACA
* *
16863 GGTAGACAAAGGATAAAGCG
66 AGTAAACAAAGGATAAAGCG
* * ** *
16883 GTTGATCAAGATTAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTGGGACTGAA-TTGAT
1 GTTGATCGAGATTAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGACT-AAGCCGAC
* * *
16947 AAGTAAACAAAGAATACAGCA
65 AAGTAAACAAAGGATAAAGCG
* * *
16968 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTTAC-TAGGGGCTGAGCCGAC
1 GTTGATCGAGATTAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTA-GGACTAAGCCGAC
**
17032 AAGTAAACAAAGGATATAAAAG
65 AAGTAAACAAAGGATA-AAGCG
* * *
17054 GTT-AACTGAGATTGAACTGACAAGTCAACAAAGGATAAAA
1 GTTGATC-GAGATTAAACCGACAAGTCAACAAAGGATAAAA
17094 AGCGATTCTT
Statistics
Matches: 178, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
84 2 0.01
85 140 0.79
86 36 0.20
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.20
Consensus pattern (85 bp):
GTTGATCGAGATTAAACCGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGACTAAGCCGACA
AGTAAACAAAGGATAAAGCG
Found at i:16915 original size:42 final size:41
Alignment explanation
Indices: 16798--17006 Score: 143
Period size: 42 Copynumber: 5.0 Consensus size: 41
16788 AGATACAAAA
16798 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGG
1 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGAT-AAAGG
* * * * * * *
16840 ATTTA-CTTAGGACTAAGCCGACAGGT-AGACAAAGGATAAAGCG
1 GTTGATC-GA-GATTAAACCGATAAGTCA-ACAAAGGATAAAG-G
* *
16883 GTTGATCAAGATTAAACCGACAAGTCAACAAAGGATAAAAGG
1 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGAT-AAAGG
* * * * * * ** * * * *
16925 ATTTACTTGGGACTGAATTGATAAGTAAACAAAGAATACAGCA
1 GTTGA-TCGAGATTAAACCGATAAGTCAACAAAGGATAAAG-G
16968 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAA
1 GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAA
17007 AGGATTTACT
Statistics
Matches: 120, Mismatches: 38, Indels: 18
0.68 0.22 0.10
Matches are distributed among these distances:
41 1 0.01
42 63 0.52
43 55 0.46
44 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (41 bp):
GTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAGG
Found at i:17031 original size:170 final size:171
Alignment explanation
Indices: 16780--17093 Score: 465
Period size: 170 Copynumber: 1.8 Consensus size: 171
16770 AACCGACAGA
16780 TAAACAAGAGATACAAAAGTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTTA
1 TAAACAAGAGATACAAAAGTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTTA
* * ** *
16845 CTTAGGACTAAGCCGACAGGTAGACAAAGGATA-AAGCGGTTGA-TCAAGATTAAACCGACAAGT
66 CTTAGGACTAAGCCGACAAGTAAACAAAGGATATAAAAGGTTAACT-AAGATTAAACCGACAAGT
16908 CAACAAAGGATAAAAGGATTTACTTGGGACTGAATTGATAAG
130 CAACAAAGGATAAAAGGATTTACTTGGGACTGAATTGATAAG
**
16950 TAAACAA-AGAATACAGCAGTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTT
1 TAAACAAGAG-ATACAAAAGTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTT
* * * * *
17014 AC-TAGGGGCTGAGCCGACAAGTAAACAAAGGATATAAAAGGTTAACTGAGATTGAACTGACAAG
65 ACTTA-GGACTAAGCCGACAAGTAAACAAAGGATATAAAAGGTTAACTAAGATTAAACCGACAAG
17078 TCAACAAAGGATAAAA
129 TCAACAAAGGATAAAA
17094 AGCGATTCTT
Statistics
Matches: 128, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
169 4 0.03
170 86 0.67
171 37 0.29
172 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (171 bp):
TAAACAAGAGATACAAAAGTTGATCGAGATTAAACCGATAAGTCAACAAAGGATAAAAGGATTTA
CTTAGGACTAAGCCGACAAGTAAACAAAGGATATAAAAGGTTAACTAAGATTAAACCGACAAGTC
AACAAAGGATAAAAGGATTTACTTGGGACTGAATTGATAAG
Found at i:17293 original size:47 final size:47
Alignment explanation
Indices: 17162--17364 Score: 214
Period size: 47 Copynumber: 4.3 Consensus size: 47
17152 AACGAGGATC
* * * *
17162 AAAAGAGTTTGACAAGG-ACTAAAGCCAATACAGTCAAACGAAAGTG
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTG
* ** * * * *
17208 AAAAGAGTTTGACCAGGTCCTAATACCAGTATAATCAAA-TAAGGGTG
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAA-GGTG
*
17255 GAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTG
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTG
* * *
17302 AAAAGAGTTTGACTAAGTCCTAACGCCAATATAGTCAAAC-AACGATG
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAA-GGTG
* *
17349 AAAAAAGTTTTACTAG
1 AAAAGAGTTTGACTAG
17365 ATACAGTTAA
Statistics
Matches: 129, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
46 20 0.16
47 107 0.83
48 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (47 bp):
AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTG
Found at i:17340 original size:94 final size:93
Alignment explanation
Indices: 17163--17340 Score: 257
Period size: 94 Copynumber: 1.9 Consensus size: 93
17153 ACGAGGATCA
*
17163 AAAGAGTTTGACAAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAGGTCC
1 AAAGAGTTTGACAAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGTCC
* *
17228 TAATACCAGTATAATCAAATAAGGGTGG
66 TAACACCAATATAATCAAATAAGGGTGG
* * * * *
17256 AAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTGAAAAGAGTTTGACTAAGTC
1 AAAGAGTTTGACAAGG-ACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGTC
* *
17321 CTAACGCCAATATAGTCAAA
65 CTAACACCAATATAATCAAA
17341 CAACGATGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 15 0.20
94 59 0.80
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (93 bp):
AAAGAGTTTGACAAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGTCC
TAACACCAATATAATCAAATAAGGGTGG
Found at i:17358 original size:94 final size:93
Alignment explanation
Indices: 17162--17364 Score: 253
Period size: 94 Copynumber: 2.2 Consensus size: 93
17152 AACGAGGATC
* *
17162 AAAAGAGTTTGACAAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAGGTC
1 AAAAGAGTTTGACTAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGTC
* * * * *
17227 CTAATACCAGTATAATCAAATAAGGGTG
66 CTAACACCAATATAATCAAACAACGATG
* * * * *
17255 GAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACGAAGGTGAAAAGAGTTTGACTAAGT
1 AAAAGAGTTTGACTAGG-ACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGT
* *
17320 CCTAACGCCAATATAGTCAAACAACGATG
65 CCTAACACCAATATAATCAAACAACGATG
* *
17349 AAAAAAGTTTTACTAG
1 AAAAGAGTTTGACTAG
17365 ATACAGTTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
93 15 0.16
94 77 0.84
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (93 bp):
AAAAGAGTTTGACTAGGACTAAAGCCAATACAGTCAAACGAAAGTGAAAAGAGTTTGACCAAGTC
CTAACACCAATATAATCAAACAACGATG
Found at i:17402 original size:35 final size:35
Alignment explanation
Indices: 17334--17529 Score: 161
Period size: 35 Copynumber: 5.8 Consensus size: 35
17324 ACGCCAATAT
* * * * * *
17334 AGTCAAACAACGATGAAAAAAGTTTTACTAGATAC
1 AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
* * ** *
17369 AGTTAAACAATGATGGGGAGAGTCTGACCAGATAC
1 AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
* * * *
17404 AGTCAAATGATTATGGACAGAGTTTGATCAGATAC
1 AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
*
17439 AGTCAAACGATGATTGAAAGAGTTTGACCAG----
1 AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
*
17470 A-T-AAACAATGATGGAAAGAGTTTGACCAGATAC
1 AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
* * * *
17503 AATCAAATGAGGATGAAAAGAGTTTGA
1 AGTCAAACGATGATGGAAAGAGTTTGA
17530 TGAAGAATGA
Statistics
Matches: 127, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
29 25 0.20
30 1 0.01
31 1 0.01
33 1 0.01
34 1 0.01
35 98 0.77
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (35 bp):
AGTCAAACGATGATGGAAAGAGTTTGACCAGATAC
Found at i:17486 original size:29 final size:29
Alignment explanation
Indices: 17443--17501 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
17433 AGATACAGTC
* *
17443 AAACGATGATTGAAAGAGTTTGACCAGAT
1 AAACAATGATGGAAAGAGTTTGACCAGAT
17472 AAACAATGATGGAAAGAGTTTGACCAGAT
1 AAACAATGATGGAAAGAGTTTGACCAGAT
17501 A
1 A
17502 CAATCAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (29 bp):
AAACAATGATGGAAAGAGTTTGACCAGAT
Done.