Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2699
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: 36295
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:170 original size:19 final size:18
Alignment explanation
Indices: 145--212 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
135 AATTCAACAA
145 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
163 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
179 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
195 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
213 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:184 original size:13 final size:13
Alignment explanation
Indices: 166--190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156 ACATAAGTGT
166 TGTATCGATACAA
1 TGTATCGATACAA
179 TGTATCGATACA
1 TGTATCGATACA
191 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:184 original size:32 final size:32
Alignment explanation
Indices: 147--209 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
137 TTCAACAATT
*
147 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
179 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
210 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:270 original size:13 final size:13
Alignment explanation
Indices: 252--276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242 CATTTTTCTG
252 TGTATCGATACAT
1 TGTATCGATACAT
265 TGTATCGATACA
1 TGTATCGATACA
277 ATCTATTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298 original size:35 final size:33
Alignment explanation
Indices: 232--299 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 33
222 GCCAAGGAAA
*
232 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
265 TGTATCGATACAATCTATTCTTTGTATCGATACAT
1 TGTATCGATAC-AT-TATTCTGTGTATCGATACAT
300 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 11 0.35
34 2 0.06
35 18 0.58
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:2763 original size:27 final size:28
Alignment explanation
Indices: 2733--2807 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
2723 ATTTTTCACA
2733 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
2760 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
2788 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
2808 TACCTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:2909 original size:52 final size:50
Alignment explanation
Indices: 2838--3011 Score: 172
Period size: 52 Copynumber: 3.4 Consensus size: 50
2828 GATTTCTCAT
*
2838 AATCGGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCC-GTTTTATT-CTAAAACACCAATTTTTCCAC
* * **
2890 AATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAA--TTTCCTTT
1 AATCGGGGATACTCCAACCC-CGTTTTATTCT-AAAACACCAATTTTTCC-AC
* * * * *
2941 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCG-TTTTA-TTCTAAAACACCAATTTTTCCAC
*
2993 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
3012 TCATTATTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
50 6 0.06
51 33 0.34
52 54 0.56
53 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (50 bp):
AATCGGGGATACTCCAACCCCGTTTTATTCTAAAACACCAATTTTTCCAC
Found at i:15630 original size:1 final size:1
Alignment explanation
Indices: 15626--15709 Score: 69
Period size: 1 Copynumber: 84.0 Consensus size: 1
15616 ATTCTTTTTC
* * * * * * * * *
15626 AAAAAAAACAAAAAAAACAACAAAAAAAAACACAAAAAAAAACAAAAAAACAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
15691 AAGAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAA
15710 TCTGCTTAAG
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:15647 original size:12 final size:11
Alignment explanation
Indices: 15626--15709 Score: 93
Period size: 11 Copynumber: 7.5 Consensus size: 11
15616 ATTCTTTTTC
15626 AAAAAAAACAA
1 AAAAAAAACAA
15637 AAAAAACAAC-A
1 AAAAAA-AACAA
15648 AAAAAAAACACA
1 AAAAAAAACA-A
15660 AAAAAAAACAA
1 AAAAAAAACAA
*
15671 AAAAACAA-AA
1 AAAAAAAACAA
*
15681 AAACAAAACAA
1 AAAAAAAACAA
15692 AGAAAAAAA-AA
1 A-AAAAAAACAA
15703 AGAAAAA
1 A-AAAAA
15710 TCTGCTTAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
10 11 0.17
11 33 0.52
12 20 0.31
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:15673 original size:33 final size:32
Alignment explanation
Indices: 15626--15709 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 32
15616 ATTCTTTTTC
15626 AAAAAAAACAAAAAAAACAACAAAAA-AAAACACA
1 AAAAAAAAC-AAAAAAACAA-AAAAACAAAACA-A
15660 AAAAAAAACAAAAAAACAAAAAAACAAAACAA
1 AAAAAAAACAAAAAAACAAAAAAACAAAACAA
*
15692 AGAAAAAAAAAAGAAAAA
1 A-AAAAAAACAA-AAAAA
15710 TCTGCTTAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
32 7 0.15
33 25 0.54
34 14 0.30
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (32 bp):
AAAAAAAACAAAAAAACAAAAAAACAAAACAA
Found at i:15689 original size:13 final size:12
Alignment explanation
Indices: 15626--15709 Score: 89
Period size: 12 Copynumber: 6.7 Consensus size: 12
15616 ATTCTTTTTC
15626 AAAAAAAACAAA
1 AAAAAAAACAAA
*
15638 AAAAACAACAAA
1 AAAAAAAACAAA
*
15650 AAAAAACACAAA
1 AAAAAAAACAAA
*
15662 AAAAAACAAAAAA
1 AAAAAA-AACAAA
15675 ACAAAAAAACAAA
1 A-AAAAAAACAAA
15688 ACAAAGAAAA-AAA
1 A-AAA-AAAACAAA
15701 AAAGAAAAA
1 AAA-AAAAA
15710 TCTGCTTAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
12 33 0.53
13 20 0.32
14 9 0.15
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:16770 original size:59 final size:59
Alignment explanation
Indices: 16678--17448 Score: 854
Period size: 55 Copynumber: 13.3 Consensus size: 59
16668 TCCGCTTTTT
*
16678 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCGCCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
**
16737 AGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
16796 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
16855 AGTCCTCAAAGAGCGGGACTCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
16914 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
16975 AGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
17034 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* * * * * **
17095 AATCCTCAAAGAGCAGGATGCC-TTTC----GAAGCTCACACAAGTTGGTGGTATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* * ** *
17150 AGTCCTCAAAGAGCAGGATGCC-TTTC----GAAGCCCACACAAGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* * * *
17205 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCAC-CTTC
* * **
17266 AGTCCCCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
17321 AGTCCTCAAAGAACAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * *
17376 AGTCCTCAAAGAGCAGGACG-----TCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
*
17431 AGTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
17449 TACACTTTAT
Statistics
Matches: 636, Mismatches: 58, Indels: 40
0.87 0.08 0.05
Matches are distributed among these distances:
51 2 0.00
54 3 0.00
55 229 0.36
56 6 0.01
59 223 0.35
60 80 0.13
61 93 0.15
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:17239 original size:171 final size:173
Alignment explanation
Indices: 16674--17449 Score: 904
Period size: 171 Copynumber: 4.5 Consensus size: 173
16664 TCCTTCCGCT
***
16674 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGC-GCCTTC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
** * **
16737 AGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCC
66 AGTCCTCAAAGAGCAGGATGCCTTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
*
16801 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC
127 TCAAAGAGCAGGACGCCTTTTC---TAAAGCCCACACAAGTTGGTGGCAC
* * * * * **
16851 CTTCAGTCCTCAAAGAGCGGGACTCCTTTTCTTTT-AAAGCCCACCCAAGTTGGTGGCA-CCTTC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
16914 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
66 AGTCCTCAAAGAGCAGGATGC-----CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* *
16979 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCAC
126 CTCAAAGAGCAGGACGCCTTTTC---TAAAGCCCACACAAGTTGGTGGCAC
* * *
17030 CTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
* * * * *
17095 AATCCTCAAAGAGCAGGATGCC-TTTCGAAGCTCACACAAGTTGGTGGTATTTTTCAGTCCTCAA
66 AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* * *
17159 AGAGCAGGATGCC-TTTC-GAAGCCCACACAAGTTGGTGGCATT
131 AGAGCAGGACGCCTTTTCTAAAGCCCACACAAGTTGGTGGCA-C
* * * *
17201 TTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
* **
17266 AGTCCCCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
66 AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* *
17330 AGAACAGGACACC-TTTC-AAAGCCCACACAAGTTGGTGGCACC
131 AGAGCAGGACGCCTTTTCTAAAGCCCACACAAGTTGGTGGCA-C
*
17372 TTTTAGTCCTCAAAGAGCAGGACG-----TC-TTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTT
*
17431 -AGTCCTCAATGAGCAGGAT
65 CAGTCCTCAAAGAGCAGGAT
17450 ACACTTTATT
Statistics
Matches: 531, Mismatches: 57, Indels: 34
0.85 0.09 0.05
Matches are distributed among these distances:
165 43 0.08
166 6 0.01
170 21 0.04
171 173 0.33
174 4 0.01
175 49 0.09
176 1 0.00
177 75 0.14
178 25 0.05
179 83 0.16
180 22 0.04
181 23 0.04
182 6 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (173 bp):
TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGACGCCTTTTCTAAAGCCCACACAAGTTGGTGGCAC
Found at i:17372 original size:29 final size:29
Alignment explanation
Indices: 17233--17374 Score: 77
Period size: 29 Copynumber: 5.1 Consensus size: 29
17223 TGCTTTTTCT
* *
17233 TTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCAAAGCCCACACAAGTTGGTGGCACC
* **
17262 TTTC--AGTCCC-CA-AAG-AGCAGGACACC
1 TTTCAAAG-CCCACACAAGTTGGTGG-CACC
*
17288 TTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *** *
17316 TTTC-CAGTCCTCA-AAGAACAG-GACACC
1 TTTCAAAGCCCACACAAG-TTGGTGGCACC
17343 TTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAAAGCCCACACAAGTTGGTGGCACC
17372 TTT
1 TTT
17375 TAGTCCTCAA
Statistics
Matches: 77, Mismatches: 24, Indels: 24
0.62 0.19 0.19
Matches are distributed among these distances:
25 3 0.04
26 15 0.19
27 18 0.23
28 18 0.23
29 20 0.26
30 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:18303 original size:19 final size:18
Alignment explanation
Indices: 18278--18345 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
18268 AATTCAACAA
18278 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
18296 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
18312 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
18328 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
18346 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:18317 original size:13 final size:13
Alignment explanation
Indices: 18299--18323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18289 ACATAAGTGT
18299 TGTATCGATACAA
1 TGTATCGATACAA
18312 TGTATCGATACA
1 TGTATCGATACA
18324 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:18317 original size:32 final size:32
Alignment explanation
Indices: 18280--18342 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
18270 TTCAACAATT
*
18280 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
18312 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
18343 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:18403 original size:13 final size:13
Alignment explanation
Indices: 18385--18410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18375 CATTTTTCTG
18385 TGTATCGATACAT
1 TGTATCGATACAT
18398 TGTATCGATACAT
1 TGTATCGATACAT
18411 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18428 original size:34 final size:33
Alignment explanation
Indices: 18365--18431 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
18355 GCCAAGGAAA
*
18365 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
18398 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
18432 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:20944 original size:28 final size:27
Alignment explanation
Indices: 20876--20946 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
20866 TTTCACAATC
20876 GGGGATACTCCAACCCCGTTAATCATCA
1 GGGGATACTCCAACCCCGTTAATCA-CA
*
20904 -GGGATACTCCAACCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTA-ATCAC-A
20931 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
20947 GTGCCTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 21 0.54
28 17 0.44
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCACA
Found at i:21007 original size:51 final size:51
Alignment explanation
Indices: 20931--21152 Score: 173
Period size: 51 Copynumber: 4.3 Consensus size: 51
20921 TTATTTCCGA
** * * * *
20931 GGGGATACTCCAACCCGTGCCTTATTCTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCG-GTTTTATTCTTAAAACACTAATTTCTCCACAATC
*
20982 GGGGATACTCCAACCTCGGTTTTATTGC-TAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACC-CGGTTTTATT-CTTAAAACACTAATTTCTCCACAATC
* * **
21034 GGGGATACT-CAACCCCGGTTTTATTTTTAAAACACCAATTT-TCCTTTAATC
1 GGGGATACTCCAA-CCCGGTTTTATTCTTAAAACACTAATTTCTCC-ACAATC
* * * ** * * *
21085 AGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAAC-CCGGTTTTA-TTCTTAAAACACTAATTTCTCCACAATC
*
21138 GAGGATACTCCAACC
1 GGGGATACTCCAACC
21153 TCGTTATTTC
Statistics
Matches: 138, Mismatches: 23, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
50 3 0.02
51 72 0.52
52 31 0.22
53 30 0.22
54 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCGGTTTTATTCTTAAAACACTAATTTCTCCACAATC
Found at i:23387 original size:20 final size:20
Alignment explanation
Indices: 23362--23415 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
23352 TCCCGTAGCC
23362 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
23382 ATGTATCGATATAATTCATA
1 ATGTATCGATACAATTCATA
23402 ATGTATCGATACAA
1 ATGTATCGATACAA
23416 ATCAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:23894 original size:79 final size:78
Alignment explanation
Indices: 23715--24038 Score: 268
Period size: 79 Copynumber: 4.1 Consensus size: 78
23705 AACGGGGCTA
* * * * * *
23715 GAGTAT-CCTCGATTATAGAAAATCGGTGTTCTGGAAATAAAATCGAGG-ATGGAATATCCCTTC
1 GAGTATCCCT-GATTGT-GAAAATCGATGTTTTAGAAATAAAATCG-GGTTTGGAGTATCCCTTC
*
23778 GGAAATAAC-AGGGTTG
63 GAAAATAACGA-GGTTG
* *
23794 GAGTATCCCTAATTATAGAAAATCGATGTTTT-GAAAATAAAATCAGGG-TTGGAGTATCCCTTC
1 GAGTATCCCTGATTGT-GAAAATCGATGTTTTAG-AAATAAAATC-GGGTTTGGAGTATCCCTTC
23857 GAAAATAACGAGGTTG
63 GAAAATAACGAGGTTG
* * * ** * *
23873 GAGTATCCCTGATCGTGGAAAATAGATGCTTTAGAAAT-AAGGCTGGGTTTGGAGTATCCCTACC
1 GAGTATCCCTGATTGT-GAAAATCGATGTTTTAGAAATAAAATC-GGGTTTGGAGTATCCCTTCG
*
23937 AAAATAACGGGGTTG
64 AAAATAACGAGGTTG
* * * * * *
23952 GAGTATCTC-GATTGTGAGAAATCAATATTTTAGAAATAATACCGGGTTTGGAGTATCCCCTC-A
1 GAGTATCCCTGATTGTGA-AAATCGATGTTTTAGAAATAAAATCGGGTTTGGAGTATCCCTTCGA
* *
24015 GAAATAACGGGGTTA
65 -AAATAACGAGGTTG
24030 GAGTATCCC
1 GAGTATCCC
24039 CGATGAAATA
Statistics
Matches: 205, Mismatches: 31, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
77 3 0.01
78 65 0.32
79 131 0.64
80 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (78 bp):
GAGTATCCCTGATTGTGAAAATCGATGTTTTAGAAATAAAATCGGGTTTGGAGTATCCCTTCGAA
AATAACGAGGTTG
Found at i:24069 original size:28 final size:28
Alignment explanation
Indices: 24002--24070 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
23992 ACCGGGTTTG
*
24002 GAGTATCCCCTCA-GAAATAACGGGGTTA
1 GAGTATCCCC-GATGAAATAACGGGGTTA
* *
24030 GAGTATCCCCGATGAAATAATGGGGTTG
1 GAGTATCCCCGATGAAATAACGGGGTTA
*
24058 GAGTATCTCCGAT
1 GAGTATCCCCGAT
24071 TGTGAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (28 bp):
GAGTATCCCCGATGAAATAACGGGGTTA
Found at i:24150 original size:51 final size:51
Alignment explanation
Indices: 24053--24169 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
24043 GAAATAATGG
* * *
24053 GGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTCAAATTAAAATCGGA
1 GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCAAAATAAAA-CGGA
* *
24105 -GTTGGATTATCCCCAATTGTGAAAAATTGGTGTTTT-AGAAATAAAACTGA
1 GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCA-AAATAAAACGGA
24155 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
24170 TCGGAAATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.07
51 53 0.93
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCAAAATAAAACGGA
Found at i:27423 original size:41 final size:41
Alignment explanation
Indices: 27155--27476 Score: 216
Period size: 41 Copynumber: 7.6 Consensus size: 41
27145 GGAAGAGGGT
** *
27155 GTCCTGCTCTTTGAGGATTAAGG-AAAAAGAGAATGAAATAG-
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGA-AATAAAAT-GC
* * * *
27196 GTCTTGCTCCTTGGGGACTAAGGAAAAAAGGAAATAAAATGC
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAA-GAAATAAAATGC
* * * * * * * *
27238 ATCATGCCCTTTGAAGACAAACGAAAAAGGAAATTAAATGT
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGC
* ** * *
27279 GTCCTGCTTTTTGAGGACAAAACAAAAAGGAGAATAAAGTGC
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGA-AATAAAATGC
* * * * *
27321 ATCATGCTCTTTGAGAACTAGAAGGGAAAAGAAGGAAATGAAGTGC
1 GTCCTGCTCTTTGAGGAC-A-AA-GGAAAA-AA-GAAATAAAATGC
* * * *
27367 GTCCCGCTTTTTGAGGACAAAGGAAAAAAGAAAAAAAAAGC
1 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGC
* * * *
27408 ATCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAATGT
1 GTCCTGCTCTTTGAGGAC-AAA-GGAAAA-AA-GAAATAAAATGC
27453 GTCCTGCTCTTTGAGGACAAAGGA
1 GTCCTGCTCTTTGAGGACAAAGGA
27477 GAGAAGGAAA
Statistics
Matches: 215, Mismatches: 53, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
41 76 0.35
42 58 0.27
43 18 0.08
44 9 0.04
45 29 0.13
46 23 0.11
47 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (41 bp):
GTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGC
Found at i:27448 original size:86 final size:86
Alignment explanation
Indices: 27210--27476 Score: 317
Period size: 86 Copynumber: 3.1 Consensus size: 86
27200 TGCTCCTTGG
* * * *
27210 GGACTAAGGAAAAAAGGAAATAAAATGCATCATGCCCTTTGAAGAC-AAA-CG-AAA-AAGGAAA
1 GGACAAAGGAAAAAA-GAAATAAAATGCATCATGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAA
*
27271 TTAAATGTGTCCTGCTTTTTGA
65 TGAAATGTGTCCTGCTTTTTGA
** * * * *
27293 GGACAAAACAAAAAGGAGAATAAAGTGCATCATGCTCTTTGAGAACTAGAAGGGAAAAGAAGGAA
1 GGACAAAGGAAAAAAGA-AATAAAATGCATCATGCTCTTTGAGGAC-AAAAGGGAAAAGAAGGAA
* * *
27358 ATGAAGTGCGTCCCGCTTTTTGA
64 ATGAAATGTGTCCTGCTTTTTGA
* * *
27381 GGACAAAGGAAAAAAGAAAAAAAAAGCATCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAT
1 GGACAAAGGAAAAAAGAAATAAAATGCATCATGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAT
*
27446 GAAATGTGTCCTGCTCTTTGA
66 GAAATGTGTCCTGCTTTTTGA
27467 GGACAAAGGA
1 GGACAAAGGA
27477 GAGAAGGAAA
Statistics
Matches: 151, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
82 2 0.01
83 35 0.23
85 2 0.01
86 47 0.31
87 26 0.17
88 39 0.26
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (86 bp):
GGACAAAGGAAAAAAGAAATAAAATGCATCATGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAT
GAAATGTGTCCTGCTTTTTGA
Found at i:27629 original size:61 final size:59
Alignment explanation
Indices: 27486--28116 Score: 541
Period size: 61 Copynumber: 10.5 Consensus size: 59
27476 AGAGAAGGAA
* * * * * *
27486 AAAGCATCCTACTCTTTGAGGACTAAAAAGTGCCA-AAACTCGTGTGGGTTTTGAAAAG
1 AAAGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* *
27544 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAG
1 -AAA-GCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAAG
* * *
27607 AAAGCATCTTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGGAG
1 AAAGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AG
* * * * *
27668 AAAACATCCTGCTGTTTGAGGACTGGAAGGTGCCATCAACTTGTGTGGGCTTTAAAAGGAG
1 AAAGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AG
* * * * *
27729 AAGGCGTCCTGA-TCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGTCTTTAAAAGGAG
1 AAAGCATCCT-ACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AG
** *
27790 AAAGCATCCTGTTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAGCATCCTACTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* * * * * * *
27849 AAAAGACGTCTTGCTCTTTAAGGACTG-AAGGTGCTACCAACTTGTGTGGGATTTAAAAGGAA
1 -AAAG-CATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AG
* ** * *
27911 AAAGCGTCCTGTTCTTTGAGGACCAGCAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAGCATCCTACTCTTTGAGGA-CTG-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* * *
27971 AAAAGGCATCCTGA-TCTTTGAGGACTG-AAGATGCCACCAGCTTGTGTGGGCTTT-GAAAG
1 -AAA-GCATCCT-ACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* * * * *
28030 --A-CGTCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTGGTGTGGGATTTAAAAGG
1 AAAGCATCCTACTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* *
28086 AGAAGACGTCCTGCTCTTTGAGGACT-AAAGG
1 A-AAG-CATCCTACTCTTTGAGGACTGAAAGG
28117 GTGAAAGGAG
Statistics
Matches: 474, Mismatches: 67, Indels: 61
0.79 0.11 0.10
Matches are distributed among these distances:
53 1 0.00
54 17 0.04
55 22 0.05
56 6 0.01
59 17 0.04
60 99 0.21
61 260 0.55
62 45 0.09
63 7 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (59 bp):
AAAGCATCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG
Found at i:27750 original size:183 final size:178
Alignment explanation
Indices: 27480--28116 Score: 720
Period size: 183 Copynumber: 3.5 Consensus size: 178
27470 CAAAGGAGAG
** * * *
27480 AAGGAAAAAGCATCCTACTCTTTGAGGACTAAAAAGTGCCA-AAACTCGTGTGGGTTTTGAAAA-
1 AAGGAAAAA-CATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGATTT-AAAAG
27543 GAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGA
64 GAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAAGA
*
27608 AAGCATCTTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGTCTTTAA
127 AAGCATCTTA-TCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * * *
27662 AAGGAGAAAACATCCTGCTGTTTGAGGACTGGAAGGTGCCATCAACTTGTGTGGGCTTTAAAAGG
1 AAGGA-AAAACATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGATTTAAAAGG
* * * * *
27727 AGAAGGCGTCCTGATCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGTCTTTAAAAGGAGAA
65 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AGAA
27792 AGCATCCTGT-TCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAA
128 AGCAT-CT-TATCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * * * *
27845 AAGGAAAAGACGTCTTGCTCTTTAAGGACT-GAAGGTGCTACCAACTTGTGTGGGATTTAAAAGG
1 AAGGAAAA-ACATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGATTTAAAAGG
* * * *
27909 AAAAAGCGTCCTGTTCTTTGAGGACCAGCAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
65 AAAAGGCGTCCTGCTCTTTGAGGA-CTG-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-A
* * *
27973 AAGGCATCCTGATCTTTGAGGACTGAAGATGCCACCAGCTTGTGTGGGCTTT--
127 AA-GCAT-CTTATCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
28025 ---GAAAGACGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGATTTAAAAGGA
1 AAGGAAAAACATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGATTTAAAAGGA
* *
28087 GAAGACGTCCTGCTCTTTGAGGACT-AAAGG
66 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
28117 GTGAAAGGAG
Statistics
Matches: 395, Mismatches: 45, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
174 3 0.01
175 1 0.00
176 19 0.05
177 54 0.14
181 5 0.01
182 118 0.30
183 189 0.48
184 5 0.01
185 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (178 bp):
AAGGAAAAACATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGATTTAAAAGGA
AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAGC
ATCTTATCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:31336 original size:9 final size:9
Alignment explanation
Indices: 31323--31358 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
31313 CAAACTCATT
*
31323 GGCTGCCAT
1 GGCTGCCAA
*
31332 GGCTGCGAA
1 GGCTGCCAA
31341 GGCTGCCAA
1 GGCTGCCAA
31350 GGCTGCCAA
1 GGCTGCCAA
31359 ACATTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.36, T:0.14
Consensus pattern (9 bp):
GGCTGCCAA
Found at i:31582 original size:39 final size:39
Alignment explanation
Indices: 31536--31687 Score: 126
Period size: 39 Copynumber: 3.7 Consensus size: 39
31526 GACCAATGTC
*
31536 GCTGGCCTTGAATTAGCACATTGGCATAAGCCCAATATT
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATT
* * * *
31575 GCTGGCCTTGAATCAGCATATTAGCATCTTGTCTTTAAGACCAATGA-C
1 GCTGGCCTTGAATCAGC-----A-CA--TTGGC-ATAAGCCCAAT-ATT
* * *
31623 ACTAGCCTTGAATCAGCACATTGGCACAAGCCCAATATT
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATT
*
31662 GCTGGCCTTGAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCACATTGGCA
31688 CCTTCATCTT
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
38 1 0.01
39 47 0.54
40 4 0.05
42 2 0.02
43 1 0.01
44 1 0.01
45 2 0.02
47 4 0.05
48 24 0.28
49 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (39 bp):
GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATT
Found at i:31615 original size:87 final size:87
Alignment explanation
Indices: 31498--31737 Score: 363
Period size: 87 Copynumber: 2.7 Consensus size: 87
31488 TGTCAGCACA
* * * * *
31498 AATCAGCATATTGGTATCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCAT
1 AATCAGCATATTGGCATCTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCAC
31563 AAGCCCAATATTGCTGGCCTTG
66 AAGCCCAATATTGCTGGCCTTG
* * *
31585 AATCAGCATATTAGCATCTTGTCTTTAAGACCAATGACACTAGCCTTGAATCAGCACATTGGCAC
1 AATCAGCATATTGGCATCTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCAC
31650 AAGCCCAATATTGCTGGCCTTG
66 AAGCCCAATATTGCTGGCCTTG
* * * *
31672 AATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCATTGGCCTTGAATCAGCACATTGGCA
1 AATCAGCATATTGGCATCTT-GTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA
31737 C
65 C
31738 CTTAACCATC
Statistics
Matches: 137, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
87 97 0.71
88 40 0.29
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (87 bp):
AATCAGCATATTGGCATCTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCAC
AAGCCCAATATTGCTGGCCTTG
Found at i:31736 original size:49 final size:49
Alignment explanation
Indices: 31654--32128 Score: 492
Period size: 49 Copynumber: 9.6 Consensus size: 49
31644 TGGCACAAGC
* * *
31654 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * **
31703 CCGATGTCATTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGT
* ** * * *
31755 CCAATGTCGCCAGCCTTGAATTAGCACATTAGCACCTTCATCTTTTAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
31804 CCGATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
31853 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
31902 CCAATGTCACT-GCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
31950 CCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * *
31999 CCGATATCGTTGTCCTTGAATCAGCATATTGGCATCTTTAACAT-TCTTAAG-
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCT-TTAAGT
* * ** * * *
32050 CCTAATGTCGCCGGCCTTGTCTCAGCACATTGTCA--TTCTTCTTCAAGT
1 CC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * *
32098 CTAATGTCGCTGGCCATGAATTAGCACATTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTG
32129 TCATTCTTCC
Statistics
Matches: 356, Mismatches: 59, Indels: 24
0.81 0.13 0.05
Matches are distributed among these distances:
47 30 0.08
48 43 0.12
49 205 0.58
50 3 0.01
51 3 0.01
52 72 0.20
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (49 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:31947 original size:97 final size:98
Alignment explanation
Indices: 31654--32032 Score: 501
Period size: 97 Copynumber: 3.8 Consensus size: 98
31644 TGGCACAAGC
* * * * *
31654 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCATTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCACTAGCCT
*
31719 TGAATCAGCACATTGGCACCTTAACCATCTTTAAGT
66 TGAATCAGCACATTGGCACCTT---CACCTTTAAGT
* ** * * * * *
31755 CCAATGTCGCCAGCCTTGAATTAGCACATTAGCACCTTCATCTTTTAGTCCGATATCGCTAGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCACTAGCCT
31820 TGAATCAGCACATTGGCACCTTCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTCACCTTTAAGT
* * * *
31853 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACT-GCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCACTAGCCT
31917 TGAATCAGCACATTGGCACCTTCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTCACCTTTAAGT
* * * *
31950 CCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATC-GTTGTCC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCACTAG-CC
*
32014 TTGAATCAGCATATTGGCA
65 TTGAATCAGCACATTGGCA
32033 TCTTTAACAT
Statistics
Matches: 242, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
96 1 0.00
97 89 0.37
98 78 0.32
101 74 0.31
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (98 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCACTAGCCT
TGAATCAGCACATTGGCACCTTCACCTTTAAGT
Found at i:31979 original size:146 final size:147
Alignment explanation
Indices: 31654--32038 Score: 538
Period size: 146 Copynumber: 2.6 Consensus size: 147
31644 TGGCACAAGC
* * * * *
31654 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCATTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
* * * * *
31719 TGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCAGCCTTGAATTAGCACAT
66 TGAATCAGCATATTGGCACCTT---TATCTTTAAGACCAATGTCGACAGCCTTGAATCAGCACAT
* *
31784 TAGCACCTTCATCTTTTAGT
128 TAGCACCTTCACCTTTAAGT
* * * * *
31804 CCGATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
* *
31869 TGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC-ACTGCCTTGAATCAGCACATTGG
66 TGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGACAGCCTTGAATCAGCACATTAG
31933 CACCTTCACCTTTAAGT
131 CACCTTCACCTTTAAGT
* *
31950 CCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGTCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
*
32015 TGAATCAGCATATTGGCATCTTTA
66 TGAATCAGCATATTGGCACCTTTA
32039 ACATTCTTAA
Statistics
Matches: 208, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
146 115 0.55
147 17 0.08
150 76 0.37
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (147 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
TGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGACAGCCTTGAATCAGCACATTAG
CACCTTCACCTTTAAGT
Found at i:32105 original size:47 final size:46
Alignment explanation
Indices: 32042--32137 Score: 129
Period size: 47 Copynumber: 2.1 Consensus size: 46
32032 ATCTTTAACA
* **
32042 TTCTTAAGCCTAATGTCGCCGGCCTTGTCTCAGCACATTGTCATTC
1 TTCTTAAGCCTAATGTCGCCGGCCATGAATCAGCACATTGTCATTC
* * *
32088 TTCTTCAAGTCTAATGTCGCTGGCCATGAATTAGCACATTGTCATTC
1 TTCTT-AAGCCTAATGTCGCCGGCCATGAATCAGCACATTGTCATTC
32135 TTC
1 TTC
32138 CCAGCTTCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 5 0.12
47 38 0.88
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (46 bp):
TTCTTAAGCCTAATGTCGCCGGCCATGAATCAGCACATTGTCATTC
Found at i:32983 original size:33 final size:33
Alignment explanation
Indices: 32941--33003 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
32931 AAGAAAATGT
32941 ATCGATACATT-ATTCAATGTATCGATACATTAC
1 ATCGATACATTGA-TCAATGTATCGATACATTAC
**
32974 ATCGATACATTGATCTTTGTATCGATACAT
1 ATCGATACATTGATCAATGTATCGATACAT
33004 CTAGGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (33 bp):
ATCGATACATTGATCAATGTATCGATACATTAC
Done.