Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3626.1
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: 114073
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 404 characters in sequence are not A, C, G, or T
Found at i:4497 original size:27 final size:27
Alignment explanation
Indices: 4467--4522 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
4457 TCATCGTGAG
*
4467 TGCTTGCATTCACCTGCATACTTTTAT
1 TGCTTGCATTCACCTGCATACTTTCAT
4494 TGCTTGCATTCACCTGCATACTTTCAT
1 TGCTTGCATTCACCTGCATACTTTCAT
4521 TG
1 TG
4523 GTCACCGTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.43
Consensus pattern (27 bp):
TGCTTGCATTCACCTGCATACTTTCAT
Found at i:6173 original size:19 final size:19
Alignment explanation
Indices: 6149--6186 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6139 CATACTGCAT
6149 TTAAATTCTAGTACGCAAG
1 TTAAATTCTAGTACGCAAG
*
6168 TTAAATTCTTGTACGCAAG
1 TTAAATTCTAGTACGCAAG
6187 CTAAGGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (19 bp):
TTAAATTCTAGTACGCAAG
Found at i:6540 original size:36 final size:36
Alignment explanation
Indices: 6496--6578 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
6486 TTAGTAGGTG
*
6496 TATATATAATATAAATATGTGTGCATGGTTTTGTT-A
1 TATATATAATATAAATATGGGTGCATGGTTTT-TTCA
*
6532 TATATATAATATAAGTATGGGTGCATGGTTTTTTCA
1 TATATATAATATAAATATGGGTGCATGGTTTTTTCA
6568 TA-A-ATAATATA
1 TATATATAATATA
6579 TATGCGTGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 8 0.18
35 3 0.07
36 33 0.75
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.45
Consensus pattern (36 bp):
TATATATAATATAAATATGGGTGCATGGTTTTTTCA
Found at i:6943 original size:40 final size:42
Alignment explanation
Indices: 6887--6983 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
6877 GCAAAAATTG
* *
6887 TAAAACACAGAGCAATAGCGACG-TTTTAC-CAAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCAACGTTTTTACTAAAAAACGCCGC
* *
6928 TAAAAACAGGGCAATAGCAACGTTTTTACTAAAAAATGCCGC
1 TAAAAACAGAGCAATAGCAACGTTTTTACTAAAAAACGCCGC
*
6970 TAAAAATAGAGCAA
1 TAAAAACAGAGCAA
6984 AAACGCCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 15 0.31
41 11 0.23
42 22 0.46
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (42 bp):
TAAAAACAGAGCAATAGCAACGTTTTTACTAAAAAACGCCGC
Found at i:7022 original size:27 final size:25
Alignment explanation
Indices: 6958--7033 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 25
6948 CGTTTTTACT
*
6958 AAAAAATGCCGCT-AAAAATAGAGC
1 AAAAAACGCCGCTAAAAAATAGAGC
*
6982 -AAAAACGCCACTAAAAAATAGAGC
1 AAAAAACGCCGCTAAAAAATAGAGC
*
7006 AATAGAAACGCCGCTAAAAACTAGAGC
1 AA-A-AAACGCCGCTAAAAAATAGAGC
7033 A
1 A
7034 TTAGCGGCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 10 0.23
24 11 0.25
25 1 0.02
26 1 0.02
27 21 0.48
ACGTcount: A:0.54, C:0.20, G:0.16, T:0.11
Consensus pattern (25 bp):
AAAAAACGCCGCTAAAAAATAGAGC
Found at i:7057 original size:41 final size:41
Alignment explanation
Indices: 7011--7147 Score: 213
Period size: 41 Copynumber: 3.3 Consensus size: 41
7001 AGAGCAATAG
*
7011 AAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTCGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGTA
* *
7052 AAACGCCGC-AAAAATCCAAAGCATTAGCGGCGCTTTCAGTA
1 AAACGCCGCTAAAAA-CCAGAGCATTAGCGGCGCTTTCGGTA
* *
7093 AAGCGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGTA
7134 AAACGCCGCTAAAA
1 AAACGCCGCTAAAA
7148 GTCATATAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 5 0.06
41 76 0.88
42 5 0.06
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (41 bp):
AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGTA
Found at i:7426 original size:14 final size:14
Alignment explanation
Indices: 7386--7447 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
7376 TTTATTTTTG
*
7386 GGTTTAGGGTTTAA
1 GGTTTATGGTTTAA
** * *
7400 TATTTAAGATTTAA
1 GGTTTATGGTTTAA
*
7414 GGTTTATGGTTTAG
1 GGTTTATGGTTTAA
7428 GGTTTTATGGTTTAA
1 GG-TTTATGGTTTAA
7443 -GTTTA
1 GGTTTA
7448 ATGGCCATGG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
13 4 0.11
14 22 0.59
15 11 0.30
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
GGTTTATGGTTTAA
Found at i:13751 original size:43 final size:42
Alignment explanation
Indices: 13703--13824 Score: 190
Period size: 43 Copynumber: 2.9 Consensus size: 42
13693 AAGTTTATAT
*
13703 TTTTTAGCGGCGTTTGTGGGAAAAGCACCGTTAAAGGTCATGG
1 TTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCAT-G
*
13746 TTTTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCATG
1 TTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
* * *
13788 TCTTTAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGG
1 TTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGG
13825 CAAAAAAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 34 0.47
43 39 0.53
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (42 bp):
TTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
Found at i:14665 original size:17 final size:17
Alignment explanation
Indices: 14645--14684 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
14635 ATTATTTTGC
*
14645 ATGAGCTGTCATTTGAT
1 ATGAACTGTCATTTGAT
* *
14662 ATGAACTGTTATTTTAT
1 ATGAACTGTCATTTGAT
14679 ATGAAC
1 ATGAAC
14685 AAATGTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (17 bp):
ATGAACTGTCATTTGAT
Found at i:14908 original size:14 final size:14
Alignment explanation
Indices: 14889--14915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14879 GTAAGAATTG
14889 TCTATATCTTTACT
1 TCTATATCTTTACT
14903 TCTATATCTTTAC
1 TCTATATCTTTAC
14916 CTGTCACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (14 bp):
TCTATATCTTTACT
Found at i:16835 original size:26 final size:27
Alignment explanation
Indices: 16806--16878 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
16796 TTTATATATT
16806 TTTTAGAATTTTTTTAAA-AATATAAA
1 TTTTAGAATTTTTTTAAATAATATAAA
* * * * *
16832 TTTTGGAATTTTTATAAATATTTTGAA
1 TTTTAGAATTTTTTTAAATAATATAAA
*
16859 TTTTAAAATTTATTTTAAAT
1 TTTTAGAATTT-TTTTAAAT
16879 TTTTGAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 16 0.43
27 14 0.38
28 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
TTTTAGAATTTTTTTAAATAATATAAA
Found at i:16847 original size:18 final size:19
Alignment explanation
Indices: 16826--16862 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16816 TTTTTAAAAA
16826 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
16844 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
16863 AAAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:16861 original size:19 final size:18
Alignment explanation
Indices: 16831--16902 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 18
16821 AAAAATATAA
16831 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTTA-AAAT
16851 ATTTTGAA-TTTTAAAATTT
1 ATTTTGAATTTTTAAAA--T
*
16870 ATTTTAAATTTTTGAAAAT
1 ATTTTGAATTTTT-AAAAT
16889 AATTTTGAATTTTT
1 -ATTTTGAATTTTT
16903 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.07
18 5 0.11
19 12 0.27
20 21 0.47
21 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
ATTTTGAATTTTTAAAAT
Found at i:20879 original size:222 final size:222
Alignment explanation
Indices: 20485--21869 Score: 2015
Period size: 222 Copynumber: 6.3 Consensus size: 222
20475 GGTTTCTCCC
* * * *
20485 CCTCCTGCTGATTCATACTAATAGTAACTGAATCAGATTCCGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
*
20550 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAGCATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
20615 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
131 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
20680 CTTTCTCTTTCTCAGCTACAATATCCA
196 CTTTCTCTTTCTCAGCTACAATATCCA
*
20707 CCTCTTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
*
20772 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAGCATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
20837 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
131 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
20902 CTTTCTCTTTCTCAGCTACAATATCCA
196 CTTTCTCTTTCTCAGCTACAATATCCA
* *
20929 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
* *
20994 ACAATGTAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCATTAACATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
* * * * *
21059 ATCAAAGCTGCCGAAGCTAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAGATATCCCGTTT
131 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
21124 CTTTCTCTTTCTCAGCTACAATATCCA
196 CTTTCTCTTTCTCAGCTACAATATCCA
* *
21151 CCTCCTGCTGATTCATAGTAAAAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
* * *
21216 ACAATGTAATTGTCATCCGATTCCACTACAACTCCATTAACAGAGTCGCTTACGTTAACATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
* *
21281 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCGCGTTCGCGCCATTGAGAAGATAGCTCGTTT
131 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
*
21346 CATTCTCTTTCTCAGCTACAATATCCA
196 CTTTCTCTTTCTCAGCTACAATATCCA
*
21373 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
21438 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCG----C-TT--C-----C
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
* * * * * * ** * * *
21491 ATCAAAGCTGCCGAAGCCGACCTCGT-TGGC-GC-CA--TT-GAG--A-AGA-TATCTCGTTTCA
131 ATCAAAGCTGCCGAAGCCAACCT--TAAGGCAACTCACGTTGGCGCCATTGAGAAGATAG-CTCG
** * * ** *
21546 TTCTCTTTCTC-AGCTACA-ATATCCACCTCCT
193 TT-TCTTTCTCTTTCT-CAGCTA-CAATATCCA
** ** * * *
21577 GTTGAT-TCAT-AGTCATAGT------AACCGAATCAGATTCCGATTTCACTTCGTGGTCTTTTT
1 CCTCCTGT--TGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTT
*
21634 CGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCATTAACATAA
64 CGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAA
21699 ACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGT
129 ACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGT
21764 TTCTTTCTCTTTCTCAGCTACAATATCCA
194 TTCTTTCTCTTTCTCAGCTACAATATCCA
21793 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
21858 ACAATGCAATTG
66 ACAATGCAATTG
21870 ATTCGGATTT
Statistics
Matches: 1038, Mismatches: 85, Indels: 80
0.86 0.07 0.07
Matches are distributed among these distances:
198 85 0.08
202 4 0.00
203 13 0.01
204 25 0.02
205 2 0.00
206 2 0.00
207 2 0.00
208 1 0.00
209 4 0.00
210 48 0.05
211 5 0.00
212 1 0.00
213 2 0.00
214 2 0.00
215 2 0.00
216 26 0.03
217 13 0.01
218 4 0.00
222 797 0.77
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (222 bp):
CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAACATAAAC
ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
CTTTCTCTTTCTCAGCTACAATATCCA
Found at i:21314 original size:444 final size:441
Alignment explanation
Indices: 20485--21869 Score: 2317
Period size: 444 Copynumber: 3.2 Consensus size: 441
20475 GGTTTCTCCC
* * * *
20485 CCTCCTGCTGATTCATACTAATAGTAACTGAATCAGATTCCGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
20550 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCGTTAGCATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCC-TTA-CATAAAC
* *
20615 ATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGGCGCCATTGAGAAGATAGCTCGTTT
129 ATCAAAGCTGCCGAAG-CAACCTTAACGCAACTCACGTTGGCGCCATTGAGAAGATATCTCGTTT
*
20680 CTTTCTCTTTCTCAGCTACAATATCCACCTCTTGTTGATTCATAGTAATAGTAACCGAATCAGAT
193 CTTTCTCTTTCTCAGCTACAATATCCACCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGAT
20745 TCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATT
258 TCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATT
*
20810 AACAGAGTCGCTTCCGTTAGCATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGT
323 AACAGAGTCGCTTCCGTTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGT
20875 TGGCGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
388 TGGCGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
20929 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
1 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
*
20994 ACAATGTAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCATTAACATAAAC
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCC-TT-ACATAAAC
* *
21059 ATCAAAGCTGCCGAAGCTAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAGATATCCCGTTT
129 ATCAAAGCTGCCGAAGC-AACCTTAACGCAACTCACGTTGGCGCCATTGAGAAGATATCTCGTTT
* *
21124 CTTTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAAAAGTAACCGAATCAGAT
193 CTTTCTCTTTCTCAGCTACAATATCCACCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGAT
* *
21189 TCGGATTTCACTTCGTGGTCTTCTTCGACAATGTAATTGTCATCCGATTCCACTACAACTCCATT
258 TCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATT
* *
21254 AACAGAGTCGCTTACGTTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCGCGT
323 AACAGAGTCGCTTCCGTTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGT
* *
21319 TCGCGCCATTGAGAAGATAGCTCGTTTCATTCTCTTTCTCAGCTACAATATCCA
388 TGGCGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
*
21373 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
1 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
21438 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCG----CTT-C-----CAT
66 ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCTTACATAAACAT
* *
21493 CAAAGCTGCCGAAG----C----CG--AC-CTCGTTGGCGCCATTGAGAAGATATCTCGTTTCAT
131 CAAAGCTGCCGAAGCAACCTTAACGCAACTCACGTTGGCGCCATTGAGAAGATATCTCGTTTCTT
* *
21547 TCTCTTTCTCAGCTACAATATCCACCTCCTGTTGATTCATAGTCATAGTAACCGAATCAGATTCC
196 TCTCTTTCTCAGCTACAATATCCACCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCG
*
21612 GATTTCACTTCGTGGTCTTTTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAAC
261 GATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAAC
*
21677 AGAGTCGCTTCCATTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGG
326 AGAGTCGCTTCCGTTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGG
21742 CGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
391 CGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
* *
21793 CCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCG
1 CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
21858 ACAATGCAATTG
66 ACAATGCAATTG
21870 ATTCGGATTT
Statistics
Matches: 901, Mismatches: 38, Indels: 28
0.93 0.04 0.03
Matches are distributed among these distances:
420 342 0.38
421 2 0.00
423 2 0.00
427 1 0.00
432 17 0.02
437 1 0.00
439 2 0.00
440 1 0.00
443 1 0.00
444 531 0.59
445 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (441 bp):
CCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCATCTTCG
ACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACAGAGTCGCTTCCTTACATAAACAT
CAAAGCTGCCGAAGCAACCTTAACGCAACTCACGTTGGCGCCATTGAGAAGATATCTCGTTTCTT
TCTCTTTCTCAGCTACAATATCCACCTCCTGTTGATTCATAGTAATAGTAACCGAATCAGATTCG
GATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAAC
AGAGTCGCTTCCGTTAACATAAACATCAAAGCTGCCGAAGCCAACCTTAAGGCAACTCACGTTGG
CGCCATTGAGAAGATAGCTCGTTTCTTTCTCTTTCTCAGCTACAATATCCA
Found at i:21885 original size:41 final size:41
Alignment explanation
Indices: 21828--21910 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
21818 AACCGAATCA
*
21828 GATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATT
1 GATTCGGATTTCACTTCGTGGTCTTCTTCGACAACGCAATT
*
21869 GATTCGGATTTCACTTCGTGTTCTTCTTCGACAACGCAATT
1 GATTCGGATTTCACTTCGTGGTCTTCTTCGACAACGCAATT
21910 G
1 G
21911 CCATCCGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (41 bp):
GATTCGGATTTCACTTCGTGGTCTTCTTCGACAACGCAATT
Found at i:22849 original size:14 final size:14
Alignment explanation
Indices: 22821--22858 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
22811 TCGAGTTTGG
*
22821 GGTTCAA-GATTTA
1 GGTTCAAGGTTTTA
22834 GGTTCAAGGTTTTA
1 GGTTCAAGGTTTTA
*
22848 GGTTCTAGGTT
1 GGTTCAAGGTT
22859 CAAGGTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (14 bp):
GGTTCAAGGTTTTA
Found at i:22936 original size:21 final size:21
Alignment explanation
Indices: 22924--22965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22914 TTCTGGATTT
*
22924 GATGTTTATGGTTTAGGTTTC
1 GATGTTTAAGGTTTAGGTTTC
22945 GATGTTTAAGGTTTGAGGTTT
1 GATGTTTAAGGTTT-AGGTTT
22966 GAGTTCAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (21 bp):
GATGTTTAAGGTTTAGGTTTC
Found at i:23206 original size:31 final size:29
Alignment explanation
Indices: 23170--23228 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
23160 GATAATGCAC
*
23170 AATGATCAAATTATTATAAATTGATAATATT
1 AATGATCAAATTATAAT-AATTGA-AATATT
*
23201 AATGATTAAATTATAATAATTGAAATAT
1 AATGATCAAATTATAATAATTGAAATAT
23229 ATGTAACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 6 0.23
31 15 0.58
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (29 bp):
AATGATCAAATTATAATAATTGAAATATT
Found at i:25626 original size:23 final size:23
Alignment explanation
Indices: 25578--25626 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
25568 TATAAAATAA
**
25578 AATATACTTAAACCAATCGATTT
1 AATATACTTAAACCAATCGAAAT
*
25601 AATATACTT-AACCAATCTTAAAT
1 AATATACTTAAACCAATC-GAAAT
25624 AAT
1 AAT
25627 TTTTATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (23 bp):
AATATACTTAAACCAATCGAAAT
Found at i:30089 original size:22 final size:22
Alignment explanation
Indices: 30064--30108 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
30054 TTTTTTTAAG
* *
30064 TTTTAATGTTTTACATTATTTA
1 TTTTAATATATTACATTATTTA
* *
30086 TTTTTATATATTATATTATTTA
1 TTTTAATATATTACATTATTTA
30108 T
1 T
30109 AATACATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAATATATTACATTATTTA
Found at i:32573 original size:26 final size:26
Alignment explanation
Indices: 32543--32595 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
32533 GCCCTTCAAT
*
32543 TTCCCTACCTGTCTTGAAACCAATAA
1 TTCCCTACATGTCTTGAAACCAATAA
32569 TTCCCTACATGTCTTGAAACCAATAA
1 TTCCCTACATGTCTTGAAACCAATAA
32595 T
1 T
32596 ATAACAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (26 bp):
TTCCCTACATGTCTTGAAACCAATAA
Found at i:44320 original size:3 final size:3
Alignment explanation
Indices: 44312--44545 Score: 75
Period size: 3 Copynumber: 75.7 Consensus size: 3
44302 GAATTAAATA
** * *
44312 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGC TGT TAT CT-T TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
44357 TAT TAC TAT TGT TAT TAC TACT TCCAT TAT TTT TAT T-T CTAAA TAT
1 TAT TAT TAT TAT TAT TAT TA-T T--AT TAT TAT TAT TAT -T-AT TAT
* * ** *
44403 TAT TTT TAT GTAT ATAT TAT TAT T-T ATAT CAT CGT TAT TAT TAC TAT
1 TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * * *
44450 TAT TAAA TAT CT-T TAT TAT TAC TAT TAT TTT TGT TCCT T-T TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
* * * * **
44496 TGTT TAT CAT CAT TA- TAT TAT TAT TAT TAC TCC TAT TAT TAT TAT
1 T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44541 CAT TA
1 TAT TA
44546 CTTCTTTTTT
Statistics
Matches: 171, Mismatches: 42, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
2 8 0.05
3 143 0.84
4 17 0.10
5 2 0.01
6 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:57796 original size:42 final size:42
Alignment explanation
Indices: 57745--57872 Score: 186
Period size: 42 Copynumber: 3.1 Consensus size: 42
57735 GAGCAGCTAA
* *
57745 AAGCCACAGCAGATCTCCTTAAAGTTTCAGTGGAATTGATCG
1 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCG
*
57787 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGG-ATTAATCG
1 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCG
* * * *
57828 AAGCTACAGTAAATCTCCTTGAAGTTTTAGTGGAATTGATTG
1 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCG
57870 AAG
1 AAG
57873 TCACATGTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 37 0.48
42 40 0.52
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (42 bp):
AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTGATCG
Found at i:57844 original size:41 final size:41
Alignment explanation
Indices: 57745--57861 Score: 162
Period size: 41 Copynumber: 2.8 Consensus size: 41
57735 GAGCAGCTAA
* * * *
57745 AAGCCACAGCAGATCTCCTTAAAGTTTCAGTGGAATTGATCG
1 AAGCTACAGCAAATCTCCTTGAAGTTTCAGTGG-ATTAATCG
*
57787 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGATTAATCG
1 AAGCTACAGCAAATCTCCTTGAAGTTTCAGTGGATTAATCG
* *
57828 AAGCTACAGTAAATCTCCTTGAAGTTTTAGTGGA
1 AAGCTACAGCAAATCTCCTTGAAGTTTCAGTGGA
57862 ATTGATTGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 38 0.55
42 31 0.45
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
AAGCTACAGCAAATCTCCTTGAAGTTTCAGTGGATTAATCG
Found at i:58159 original size:23 final size:24
Alignment explanation
Indices: 58122--58167 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
58112 AATTTTGGGC
58122 CCAAAACCCCTAAACCC-ACTAAG
1 CCAAAACCCCTAAACCCTACTAAG
58145 CCAATAACCCC-AAACCCTACTAA
1 CCAA-AACCCCTAAACCCTACTAA
58168 ACCCAGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.43, C:0.43, G:0.02, T:0.11
Consensus pattern (24 bp):
CCAAAACCCCTAAACCCTACTAAG
Found at i:58891 original size:35 final size:35
Alignment explanation
Indices: 58845--58911 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
58835 ATTTTTTTTT
58845 CCAAAAAAATTGACTTATATAAGCCCCCAAAACGA
1 CCAAAAAAATTGACTTATATAAGCCCCCAAAACGA
*
58880 CCAAAAAAATTGACTTATATAGGCCCCCAAAA
1 CCAAAAAAATTGACTTATATAAGCCCCCAAAA
58912 TGACGTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (35 bp):
CCAAAAAAATTGACTTATATAAGCCCCCAAAACGA
Found at i:68368 original size:32 final size:32
Alignment explanation
Indices: 68332--68575 Score: 319
Period size: 32 Copynumber: 7.6 Consensus size: 32
68322 TGAAAGGGTG
*
68332 ACACTTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
68364 ACACTTGAAAAGGATTTGTAGACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
68396 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** * *
68428 ACACTTGAAAAGGAAACATTCACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
68460 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
68492 GCACTTGAAAAGGAAATGTAC-CTTTTGTGTGC
1 ACACTTGAAAAGGAAATGTACAC-TTTGTGTGT
68524 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
68556 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
68576 GCACCTCGGG
Statistics
Matches: 184, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
31 1 0.01
32 166 0.90
33 17 0.09
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:68469 original size:96 final size:96
Alignment explanation
Indices: 68332--68569 Score: 361
Period size: 96 Copynumber: 2.5 Consensus size: 96
68322 TGAAAGGGTG
*
68332 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTAGACTTTGTGTGTA
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
** *
68397 CACTTGAAAAGGATTTGTACAC-TTTGTGTGT
66 CACTTGAAAAGGAAATGTAC-CTTTTGTGTGC
* * * *
68428 ACACTTGAAAAGGAAACATTCACTTTGTATGTACACTTGAAAAGGATTTGTACACTTTGTGTGTG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
68493 CACTTGAAAAGGAAATGTACCTTTTGTGTGC
66 CACTTGAAAAGGAAATGTACCTTTTGTGTGC
* *
68524 ACACTTGAAAAGGAAATGTACACTTTGTGTGTACCATTTGAAAAGG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTA-CACTTGAAAAGG
68570 GAATGTGCAC
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
95 1 0.01
96 115 0.91
97 11 0.09
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (96 bp):
ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
CACTTGAAAAGGAAATGTACCTTTTGTGTGC
Found at i:69644 original size:31 final size:31
Alignment explanation
Indices: 69601--69673 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
69591 TGTCCCAAGT
*
69601 CACAAGGGCGTGTGTAATCACACTGCCTGAC
1 CACAAGGGCGTGTGTAATCACACGGCCTGAC
* * *
69632 CACATGGGCGTGTGTAATCACTCGGCCTGGC
1 CACAAGGGCGTGTGTAATCACACGGCCTGAC
*
69663 CACACGGGCGT
1 CACAAGGGCGT
69674 ATGTGGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (31 bp):
CACAAGGGCGTGTGTAATCACACGGCCTGAC
Found at i:72777 original size:5 final size:5
Alignment explanation
Indices: 72767--72793 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
72757 AAAATCTGTG
72767 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
72794 TAACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:77192 original size:5 final size:5
Alignment explanation
Indices: 77182--77209 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
77172 CTGTGTGTTC
77182 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
77210 TCACATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:77580 original size:72 final size:72
Alignment explanation
Indices: 77481--77670 Score: 245
Period size: 72 Copynumber: 2.6 Consensus size: 72
77471 CTCGCATTTA
* * * *
77481 AGCTACTCACGGGCTTGTTCACAAAGTTAGCACCCCGACCCACATAGCATTATCATGTAATGCTC
1 AGCTACTCACGGGCCTG-TCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTC
*
77546 GCTCATCG
65 GCTCAACG
* * * **
77554 AGCTACTCAAGGTCCTGTCACGAAGTTAATACCCGGACCCACATAGCATTAACATGAAATGCTCG
1 AGCTACTCACGGGCCTGTCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTCG
*
77619 TTCAACG
66 CTCAACG
* *
77626 AGTTACTCACGGGCCTAATCACAAAGTTAGCACCCGGACCCACAT
1 AGCTACTCACGGGCCT-GTCACAAAGTTAGCACCCGGACCCACAT
77671 TACATGTATC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 60 0.61
73 38 0.39
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (72 bp):
AGCTACTCACGGGCCTGTCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTCG
CTCAACG
Found at i:84501 original size:7 final size:7
Alignment explanation
Indices: 84479--84519 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
84469 TTTGAGTCCC
84479 TTTTAT-
1 TTTTATA
84485 TTTTAT-
1 TTTTATA
84491 TTTTATA
1 TTTTATA
84498 TTTTATA
1 TTTTATA
84505 TTTTATA
1 TTTTATA
84512 TTTT-TA
1 TTTTATA
84518 TT
1 TT
84520 ATTTATTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTATA
Found at i:84501 original size:14 final size:14
Alignment explanation
Indices: 84482--84539 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
84472 GAGTCCCTTT
84482 TATTTTTATTTTTA
1 TATTTTTATTTTTA
84496 TA-TTTTATATTTTA
1 TATTTTTAT-TTTTA
84510 TATTTTTATTATTTA
1 TATTTTTATT-TTTA
*
84525 TTATCTCTTATTTTT
1 -TAT-TTTTATTTTT
84540 TTTGGAGACT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 6 0.16
14 10 0.26
15 10 0.26
16 6 0.16
17 6 0.16
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTATTTTTA
Found at i:84524 original size:15 final size:15
Alignment explanation
Indices: 84482--84525 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
84472 GAGTCCCTTT
84482 TATTTTTATT-TTTA
1 TATTTTTATTATTTA
84496 TA-TTTTA-TATTTTA
1 TATTTTTATTA-TTTA
84510 TATTTTTATTATTTA
1 TATTTTTATTATTTA
84525 T
1 T
84526 TATCTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.04
13 5 0.19
14 8 0.31
15 10 0.38
16 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTTATTATTTA
Found at i:85540 original size:4 final size:4
Alignment explanation
Indices: 85533--85571 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
85523 AAAAATATAT
85533 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
85572 TTGGTAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:86405 original size:30 final size:30
Alignment explanation
Indices: 86371--86427 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
86361 TAGGCACGTC
* *
86371 CACACGGGTAAACCACACGCCTGTGTGAGG
1 CACACGGGCAAACCACACGCCCGTGTGAGG
* *
86401 CACACGGGCAGACCACATGCCCGTGTG
1 CACACGGGCAAACCACACGCCCGTGTG
86428 TCATGGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.12
Consensus pattern (30 bp):
CACACGGGCAAACCACACGCCCGTGTGAGG
Found at i:86834 original size:156 final size:156
Alignment explanation
Indices: 86550--86844 Score: 590
Period size: 156 Copynumber: 1.9 Consensus size: 156
86540 TAAAATCTAA
86550 TGGTCATTTTGAACAAAAAAAATTCAACAATCCACTGACAAATTACACAACTGTCAACAAAAAGT
1 TGGTCATTTTGAACAAAAAAAATTCAACAATCCACTGACAAATTACACAACTGTCAACAAAAAGT
86615 ATTTCATTATTCCACATCATACCACTGTTTGTATCTTCTTTGCATAAGCTTCAAAATCCCAAAAG
66 ATTTCATTATTCCACATCATACCACTGTTTGTATCTTCTTTGCATAAGCTTCAAAATCCCAAAAG
86680 AAAACACTAAATCTATTGGTAGTAAT
131 AAAACACTAAATCTATTGGTAGTAAT
86706 TGGTCATTTTGAACAAAAAAAATTCAACAATCCACTGACAAATTACACAACTGTCAACAAAAAGT
1 TGGTCATTTTGAACAAAAAAAATTCAACAATCCACTGACAAATTACACAACTGTCAACAAAAAGT
86771 ATTTCATTATTCCACATCATACCACTGTTTGTATCTTCTTTGCATAAGCTTCAAAATCCCAAAAG
66 ATTTCATTATTCCACATCATACCACTGTTTGTATCTTCTTTGCATAAGCTTCAAAATCCCAAAAG
86836 AAAACACTA
131 AAAACACTA
86845 TACATACATA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 139 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (156 bp):
TGGTCATTTTGAACAAAAAAAATTCAACAATCCACTGACAAATTACACAACTGTCAACAAAAAGT
ATTTCATTATTCCACATCATACCACTGTTTGTATCTTCTTTGCATAAGCTTCAAAATCCCAAAAG
AAAACACTAAATCTATTGGTAGTAAT
Found at i:86853 original size:4 final size:4
Alignment explanation
Indices: 86844--86890 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
86834 AGAAAACACT
86844 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
86891 TTGGTAGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:87725 original size:30 final size:30
Alignment explanation
Indices: 87690--87746 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
87680 TAGGCACGTC
*
87690 CACACGGGTAAACCACACACCCGTGTGAGG
1 CACACGGGCAAACCACACACCCGTGTGAGG
* **
87720 CACACGGGCAGACCACATGCCCGTGTG
1 CACACGGGCAAACCACACACCCGTGTG
87747 TCATGACCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.28, T:0.11
Consensus pattern (30 bp):
CACACGGGCAAACCACACACCCGTGTGAGG
Found at i:97365 original size:32 final size:32
Alignment explanation
Indices: 97329--97572 Score: 319
Period size: 32 Copynumber: 7.6 Consensus size: 32
97319 TGAAAGGGTG
*
97329 ACACTTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
97361 ACACTTGAAAAGGATTTGTAGACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
97393 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** * *
97425 ACACTTGAAAAGGAAACATTCACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
97457 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
97489 GCACTTGAAAAGGAAATGTAC-CTTTTGTGTGC
1 ACACTTGAAAAGGAAATGTACAC-TTTGTGTGT
97521 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
97553 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
97573 GCACCTCGGG
Statistics
Matches: 184, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
31 1 0.01
32 166 0.90
33 17 0.09
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:97466 original size:96 final size:96
Alignment explanation
Indices: 97329--97566 Score: 361
Period size: 96 Copynumber: 2.5 Consensus size: 96
97319 TGAAAGGGTG
*
97329 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTAGACTTTGTGTGTA
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
** *
97394 CACTTGAAAAGGATTTGTACAC-TTTGTGTGT
66 CACTTGAAAAGGAAATGTAC-CTTTTGTGTGC
* * * *
97425 ACACTTGAAAAGGAAACATTCACTTTGTATGTACACTTGAAAAGGATTTGTACACTTTGTGTGTG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
97490 CACTTGAAAAGGAAATGTACCTTTTGTGTGC
66 CACTTGAAAAGGAAATGTACCTTTTGTGTGC
* *
97521 ACACTTGAAAAGGAAATGTACACTTTGTGTGTACCATTTGAAAAGG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTA-CACTTGAAAAGG
97567 GAATGTGCAC
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
95 1 0.01
96 115 0.91
97 11 0.09
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (96 bp):
ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
CACTTGAAAAGGAAATGTACCTTTTGTGTGC
Found at i:98641 original size:31 final size:31
Alignment explanation
Indices: 98598--98670 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
98588 TGTCCCAAGT
*
98598 CACAAGGGCGTGTGTAATCACACTGCCTGAC
1 CACAAGGGCGTGTGTAATCACACGGCCTGAC
* * *
98629 CACATGGGCGTGTGTAATCACTCGGCCTGGC
1 CACAAGGGCGTGTGTAATCACACGGCCTGAC
*
98660 CACACGGGCGT
1 CACAAGGGCGT
98671 ATGTGGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (31 bp):
CACAAGGGCGTGTGTAATCACACGGCCTGAC
Found at i:101774 original size:5 final size:5
Alignment explanation
Indices: 101764--101790 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
101754 AAAATCTGTG
101764 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
101791 TAACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:106189 original size:5 final size:5
Alignment explanation
Indices: 106179--106206 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
106169 CTGTGTGTTC
106179 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
106207 TCACATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:106577 original size:72 final size:72
Alignment explanation
Indices: 106478--106667 Score: 245
Period size: 72 Copynumber: 2.6 Consensus size: 72
106468 CTCGCATTTA
* * * *
106478 AGCTACTCACGGGCTTGTTCACAAAGTTAGCACCCCGACCCACATAGCATTATCATGTAATGCTC
1 AGCTACTCACGGGCCTG-TCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTC
*
106543 GCTCATCG
65 GCTCAACG
* * * **
106551 AGCTACTCAAGGTCCTGTCACGAAGTTAATACCCGGACCCACATAGCATTAACATGAAATGCTCG
1 AGCTACTCACGGGCCTGTCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTCG
*
106616 TTCAACG
66 CTCAACG
* *
106623 AGTTACTCACGGGCCTAATCACAAAGTTAGCACCCGGACCCACAT
1 AGCTACTCACGGGCCT-GTCACAAAGTTAGCACCCGGACCCACAT
106668 TACATGTATC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 60 0.61
73 38 0.39
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (72 bp):
AGCTACTCACGGGCCTGTCACAAAGTTAGCACCCGGACCCACATAGCATTAACATGAAATGCTCG
CTCAACG
Found at i:113505 original size:15 final size:15
Alignment explanation
Indices: 113478--113531 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
113468 TGAGTCCCTT
113478 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
113493 -TATTTTATATTTTTA
1 TTATTTT-TATTTTTA
*
113508 TTATTTATTATCTCTTA
1 TTATTT-TTAT-TTTTA
113525 TT-TTTTT
1 TTATTTTT
113532 TGGAGACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 6 0.18
15 10 0.29
16 11 0.32
17 7 0.21
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Done.