Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003779.1 Hibiscus syriacus cultivar Beakdansim tig00008089_pilon, 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: 79433
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5963 original size:15 final size:15
Alignment explanation
Indices: 5952--5980 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5942 ACTCAAAAAG
5952 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
5967 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
5981 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:11996 original size:19 final size:19
Alignment explanation
Indices: 11972--12011 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11962 ACACTTCTCC
11972 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
11991 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
12010 CA
1 CA
12012 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:14581 original size:19 final size:20
Alignment explanation
Indices: 14557--14595 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
14547 CTATTTTTTT
14557 CAAAAAA-ACAAAAAAAAAA
1 CAAAAAAGACAAAAAAAAAA
*
14576 CAAAAAAGGCAAAAAAAAAA
1 CAAAAAAGACAAAAAAAAAA
14596 AACGGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (20 bp):
CAAAAAAGACAAAAAAAAAA
Found at i:14589 original size:16 final size:18
Alignment explanation
Indices: 14569--14615 Score: 73
Period size: 16 Copynumber: 2.8 Consensus size: 18
14559 AAAAAACAAA
14569 AAAAAAACAAAAAA-GGC
1 AAAAAAACAAAAAACGGC
14586 -AAAAAA-AAAAAACGGC
1 AAAAAAACAAAAAACGGC
14602 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
14616 AGAGCCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.22
16 9 0.33
17 6 0.22
18 6 0.22
ACGTcount: A:0.81, C:0.11, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAACGGC
Found at i:14605 original size:24 final size:22
Alignment explanation
Indices: 14558--14616 Score: 59
Period size: 24 Copynumber: 2.7 Consensus size: 22
14548 TATTTTTTTC
14558 AAAAAAAC--AAAAAAAAAACA
1 AAAAAAACAAAAAAAAAAAACA
** *
14578 AAAAAGGCAAAAAAAAAAAACGGC
1 AAAAAAACAAAAAAAAAAAAC--A
14602 AAAAAAACAAAAAAA
1 AAAAAAACAAAAAAA
14617 GAGCCAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.20
22 11 0.37
24 13 0.43
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAAAACA
Found at i:22587 original size:30 final size:30
Alignment explanation
Indices: 22552--22614 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
22542 TTAAATTCGA
**
22552 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
22582 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
22612 ATG
1 ATG
22615 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:28765 original size:3 final size:3
Alignment explanation
Indices: 28757--28811 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
28747 TTGTATTAAC
*
28757 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AATT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AAT AAT AAT
*
28804 AGT AAT AA
1 AAT AAT AA
28812 ATTAAAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28825 original size:29 final size:29
Alignment explanation
Indices: 28757--28813 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
28747 TTGTATTAAC
*
28757 AATAA-TAATAATAATAATAATAATAAAT
1 AATAATTAAAAATAATAATAATAATAAAT
*
28785 AATAATTAAAAATAATAATAGTAATAAAT
1 AATAATTAAAAATAATAATAATAATAAAT
28814 TAAAATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AATAATTAAAAATAATAATAATAATAAAT
Found at i:32623 original size:16 final size:16
Alignment explanation
Indices: 32602--32639 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32592 AAAAATAATT
32602 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
32618 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
32634 T-ATAAA
1 TAATAAA
32640 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:32858 original size:21 final size:21
Alignment explanation
Indices: 32803--32858 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
32793 TTATATACGT
*
32803 TAATAGTAAAATAATAATAAATA
1 TAATAGTAATA-AAT-ATAAATA
*
32826 TAATAGTTATAAATATAAATA
1 TAATAGTAATAAATATAAATA
32847 TATATA-TAATAA
1 TA-ATAGTAATAA
32859 CTTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 14 0.48
22 6 0.21
23 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
TAATAGTAATAAATATAAATA
Found at i:33371 original size:35 final size:36
Alignment explanation
Indices: 33301--33400 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
33291 GTGCTTGTGG
* * *
33301 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
33338 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
33373 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
33401 TAGGACAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:34167 original size:106 final size:105
Alignment explanation
Indices: 33861--34580 Score: 630
Period size: 109 Copynumber: 6.9 Consensus size: 105
33851 AATATTGTTC
* * * * * *
33861 CGAGTTCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTAAAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAAATGTTTGTTGACA
** ** * * *
33926 GTCAGCCACCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
33967 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA--CG-AAAT-CTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
* * *
34027 TCAGCCGTCCCTTCATTATGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
34067 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAAATGTTTGTTGACA
34132 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** * *
34173 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCGAATGAAACT-GAAAAGTTGTTCG
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAATTGGAAAA--TGTTTG
* *
34235 TTGACAACCAACCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCT
59 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
34282 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCT-AGAATTGGGAAATTGTTTGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGA-AATT-GGAAAATGTTTGT
* *
34345 TGACAACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
60 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
34391 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGTTTGGCTCCGAAA-T------TGCTTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
* * * * * *
34449 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
34489 TGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAACTGGGAAAT-TATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGT-TTGTTGACA
34553 ACCAGCCGTCCCTTCGTTGTGAAGTTGA
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGA
34581 GATTGGCTCC
Statistics
Matches: 504, Mismatches: 83, Indels: 55
0.79 0.13 0.09
Matches are distributed among these distances:
98 82 0.16
99 1 0.00
100 79 0.16
101 5 0.01
102 1 0.00
105 39 0.08
106 113 0.22
107 7 0.01
108 7 0.01
109 164 0.33
110 2 0.00
111 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:34394 original size:218 final size:205
Alignment explanation
Indices: 33861--34580 Score: 616
Period size: 206 Copynumber: 3.4 Consensus size: 205
33851 AATATTGTTC
* * * * *
33861 CGAGTTCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTAAAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTAGAATTGGGAAATTGTTTGTTGACA
** ** * * *
33926 GTCAGCCACCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGA
65 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
* ** * *
33991 AGATGAAATTGACTCTGAACGAAATCTTGTTGACAATCAGCCGTCCCTTCATTATGAAGTTGAAC
130 AGATGAAATCGACAATGAACGAAATCTTGTTGACAACCAACCGTCCCTTCATTATGAAGTTGAAC
34056 TTGTGTTGTCT
195 TTGTGTTGTCT
* * * *
34067 CGAGTCCAATATCCTTCGC-TGCGAAGTTGAAATTGGCTCT-GAAATTTGAAAAATGTTTGTTGA
1 CGAGTCCAATATCCTCCGCGTG-G-AGTTGAAATTGGCTCTAG-AATTGGGAAATTGTTTGTTGA
*
34130 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCCTCCG
63 CAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTCCG
* * * *
34194 -TCGTGGAGTTGAAATCG-CGAATGAAACTGAAAAGTTGTTCGTTGACAACCAACCGTCCCTTCG
124 CT-GTGAAGATGAAATCGAC-AATG-AAC-G-AAA--TCTT-GTTGACAACCAACCGTCCCTTCA
34257 TTATGAAGTTGAACTTGTGTTGTCT
181 TTATGAAGTTGAACTTGTGTTGTCT
* * *
34282 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTAGAATTGGGAAATTGTTTGTTG
1 CGAGT--C-CAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTAGAATTGGGAAATTGTTTGTTG
* * *
34347 ACAACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTG
62 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTG
* ** * * * * ** ** * ** *
34412 TGAAGTTGAGTTTGGC--T--CCGAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGTGAAGT
127 TGAAGATGAAATCGACAATGAACGAAA-T-CTTGTTGACAACCAACCGTCCCTTCATTATGAAGT
* *
34473 TGAGCTTGTGCTGTCT
190 TGAACTTGTGTTGTCT
* * * * * * * * *
34489 TGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCT-GAAACTGGGAAATT-ATTGTTGAC
1 CGAGTCCAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTAG-AATTGGGAAATTGTTTGTTGAC
*
34552 AACCAGCCGTCCCTTCGTTGTGAAGTTGA
64 AACCAGCCGTCCCTTCGCTGTGAAGTTGA
34581 GATTGGCTCC
Statistics
Matches: 423, Mismatches: 65, Indels: 55
0.78 0.12 0.10
Matches are distributed among these distances:
203 36 0.09
204 39 0.09
205 1 0.00
206 90 0.21
207 45 0.11
208 8 0.02
209 24 0.06
210 4 0.01
211 1 0.00
212 3 0.01
213 1 0.00
214 3 0.01
215 69 0.16
216 3 0.01
217 2 0.00
218 89 0.21
219 3 0.01
220 2 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (205 bp):
CGAGTCCAATATCCTCCGCGTGGAGTTGAAATTGGCTCTAGAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAA
GATGAAATCGACAATGAACGAAATCTTGTTGACAACCAACCGTCCCTTCATTATGAAGTTGAACT
TGTGTTGTCT
Found at i:34502 original size:98 final size:98
Alignment explanation
Indices: 34333--34516 Score: 278
Period size: 98 Copynumber: 1.9 Consensus size: 98
34323 CTAGAATTGG
* * * *
34333 GAAATTGTTTGTTGACAACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGCTTGTCGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
*
34398 AATATCCTTCGCTGTGAAGTTGAGTTTGGCTCC
66 AATATCCTTCGATGTGAAGTTGAGTTTGGCTCC
** * * *
34431 GAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGCTTGTCGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
34496 AATATCCTTCGATGTGAAGTT
66 AATATCCTTCGATGTGAAGTT
34517 AAAATTGGCC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 76 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.35
Consensus pattern (98 bp):
GAAATTGCTTGTCGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
AATATCCTTCGATGTGAAGTTGAGTTTGGCTCC
Found at i:34674 original size:160 final size:160
Alignment explanation
Indices: 34403--34740 Score: 622
Period size: 160 Copynumber: 2.1 Consensus size: 160
34393 AGTCCAATAT
* * *
34403 CCTTCGCTGTGAAGTTGAGTTTGGCTCCGAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
34468 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
34533 CTGGGAAATTATTGTTGACAACCAGCCGTC
131 CTGGGAAATTATTGTTGACAACCAGCCGTC
* *
34563 CCTTCGTTGTGAAGTTGAGATTGGCTCCGCAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
*
34628 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
34693 CTGGGAAATTATTGTTGACAACCAGCCGTC
131 CTGGGAAATTATTGTTGACAACCAGCCGTC
34723 CCTTCGTTGTGAAGTTGA
1 CCTTCGTTGTGAAGTTGA
34741 ACTTGTGTTG
Statistics
Matches: 172, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
160 172 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (160 bp):
CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
CTGGGAAATTATTGTTGACAACCAGCCGTC
Found at i:35346 original size:65 final size:65
Alignment explanation
Indices: 35242--35422 Score: 308
Period size: 65 Copynumber: 2.8 Consensus size: 65
35232 GACAAAATTT
35242 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
35307 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
35372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
35423 CTATCTCAAG
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 95 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:35413 original size:102 final size:102
Alignment explanation
Indices: 35307--35662 Score: 604
Period size: 102 Copynumber: 3.5 Consensus size: 102
35297 TCAATGTTTA
* *
35307 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
35372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
35409 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
35474 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
35511 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
35576 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
35613 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
35663 CTGTCTCAAG
Statistics
Matches: 237, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 237 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:35423 original size:37 final size:37
Alignment explanation
Indices: 35372--35680 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
35362 TCAATGTTTA
* *
35372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
35409 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
35445 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
35473 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
35511 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
35547 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
35575 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
35613 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
35649 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
35681 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 25 0.12
30 8 0.04
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 66 0.32
37 87 0.42
38 7 0.03
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:35584 original size:50 final size:50
Alignment explanation
Indices: 35428--35587 Score: 124
Period size: 50 Copynumber: 3.2 Consensus size: 50
35418 GGAAACTATC
* *
35428 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
* *** * ** * * * * *** * *
35478 TCAAGAGAAAC-TGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATC
1 TCAAGAGAGACAAAACTCATTTCA-AGGGAAATGT-TTTCAATGTTTA-TGTT
35530 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
35580 TCAAGAGA
1 TCAAGAGA
35588 AACTGTCTCA
Statistics
Matches: 72, Mismatches: 34, Indels: 8
0.63 0.30 0.07
Matches are distributed among these distances:
49 5 0.07
50 27 0.38
51 15 0.21
52 19 0.26
53 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (50 bp):
TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
Found at i:36573 original size:22 final size:22
Alignment explanation
Indices: 36548--36596 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
36538 TTGTGTTTGG
36548 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
36570 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
36592 TCAAA
1 TCAAA
36597 TGATTGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:37232 original size:20 final size:21
Alignment explanation
Indices: 37207--37266 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
37197 TTTTGTCCCT
*
37207 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
37227 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
37248 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
37267 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:37277 original size:22 final size:22
Alignment explanation
Indices: 37223--37275 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
37213 ATTTTTGTTC
37223 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
37244 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
37267 TTTCTTTTT
1 TTTCTTTTT
37276 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:40633 original size:16 final size:16
Alignment explanation
Indices: 40614--40651 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40604 AAAAAAAATT
40614 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
40630 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
40646 T-ATAAA
1 TAATAAA
40652 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:41380 original size:35 final size:35
Alignment explanation
Indices: 41310--41409 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
41300 GTGCTTGTGG
* * *
41310 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAG-TTGAATCCTAGCAAAATTCT
*
41347 ATCCTATTTTAGGAGTTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTGAATCCTAGCAAAATTCT
*
41382 ATCCTATTTTTGAGAGTTGGAATCCTAG
1 ATCCTATTTTAG-GAGTT-GAATCCTAG
41410 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 13 0.23
37 16 0.29
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (35 bp):
ATCCTATTTTAGGAGTTGAATCCTAGCAAAATTCT
Found at i:43607 original size:21 final size:22
Alignment explanation
Indices: 43578--43619 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43568 AAGTAACGAA
*
43578 TACATGAAA-TATTAAAATTAT
1 TACAAGAAATTATTAAAATTAT
43599 TACAAGAAATTATTAAAATTA
1 TACAAGAAATTATTAAAATTA
43620 GTTTGACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAGAAATTATTAAAATTAT
Found at i:44373 original size:14 final size:15
Alignment explanation
Indices: 44356--44387 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
44346 AAAATAAATA
44356 TTAAAATAAT-TTAT
1 TTAAAATAATATTAT
44370 TTAAAATAATATTAT
1 TTAAAATAATATTAT
44385 TTA
1 TTA
44388 TTATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAATAATATTAT
Found at i:45813 original size:3 final size:3
Alignment explanation
Indices: 45805--45861 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
45795 GGCCTGGTTG
* *
45805 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
45851 TAA TAA TAA TA
1 TAA TAA TAA TA
45862 TAAATAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:45822 original size:9 final size:9
Alignment explanation
Indices: 45808--45868 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
45798 CTGGTTGTAA
45808 TAATAATAT
1 TAATAATAT
*
45817 TAATAATAA
1 TAATAATAT
*
45826 AAATATATAAT
1 TAATA-AT-AT
*
45837 AAATAATA-
1 TAATAATAT
*
45845 TAATAATAA
1 TAATAATAT
45854 TAATAATAT
1 TAATAATAT
*
45863 AAATAA
1 TAATAA
45869 AACCGGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
9 26 0.60
10 4 0.09
11 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAATAATAT
Found at i:45867 original size:12 final size:12
Alignment explanation
Indices: 45806--45868 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
45796 GCCTGGTTGT
*
45806 AATAATAATATT
1 AATAATAATATA
*
45818 AATAATAAAAATA
1 AATAAT-AATATA
*
45831 TATAATAA-AT-
1 AATAATAATATA
45841 AAT-ATAATA-A
1 AATAATAATATA
45851 TAATAATAATATA
1 -AATAATAATATA
45864 AATAA
1 AATAA
45869 AACCGGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 5 0.12
12 19 0.46
13 10 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATAATATA
Found at i:46436 original size:113 final size:113
Alignment explanation
Indices: 46094--46991 Score: 1153
Period size: 113 Copynumber: 8.0 Consensus size: 113
46084 CAGAGTTATG
* * * *
46094 CAAAAGGCTGAACAAACTCTTCTCATTGTGAA---CTTCTTC-TTCTTCAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
* *
46155 TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
46203 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TT-TTC-TTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGAT---GAGTTCTTC
* * * * * * * * *
46264 TTATTATGAACTGTAC-CTGGCAATGTTAATCCATTAATTGATGAATTTAAA
63 TCATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
*
46315 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
*
46380 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
* *
46428 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTTTTTTCAGATGAGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-C-TTTCTTCAGATGAGTTCTTCT
* * * * *
46493 CATTATGAACTTTCTCTGGCAAAGTTAATCCATCAATTGATGAATTTAAA
64 CATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
*
46543 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
**** * *
46608 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
* *
46656 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
* *
46721 TTATGAACTTTCTCTGGAAAAGTTGATCCAT--TGTTATGGATTTGAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
* *
46767 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-TCTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCT-TTCTTCAGATGAGTTCTTCTC
* * * * * * **
46831 ATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTCAAA
65 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
* *
46880 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
* *
46945 TTATGAACTCTTC-C-GGAAATGTTGATCCATTGAA-TGATGGATTTGAA
66 TTATGAACT-TTCTCTGGAAAAGTTGATCCA-TCAAGTGATGGATTTGAA
46992 TCTTTGCTAA
Statistics
Matches: 693, Mismatches: 77, Indels: 35
0.86 0.10 0.04
Matches are distributed among these distances:
109 41 0.06
110 2 0.00
111 98 0.14
112 104 0.15
113 326 0.47
114 5 0.01
115 107 0.15
116 10 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAA
Found at i:46592 original size:228 final size:224
Alignment explanation
Indices: 46094--46953 Score: 1182
Period size: 228 Copynumber: 3.8 Consensus size: 224
46084 CAGAGTTATG
* * * *
46094 CAAAAGGCTGAACAAACTCTTCTCATTGTGAA---CTTCTT-CTTCTTCAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
46155 TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAT
* *
46220 TCTTCTCATTATGAA-TT-TT-TTCTTCTTCAGATGACGAGTTCTTCTTATTATGAACTGTAC-C
131 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTC
*
46281 TGGCAATGTTAATCCATTAATTGATGAATTTAAA
192 TGGCAAAGTTAATCCA-TAATTGATGAATTTAAA
* *
46315 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
46380 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAT
* *
46445 TCTTCTCATTATGAACTTCTTATTCCTTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
131 TCTTCTCATTATGAACTTCTTCTT-C--TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
46510 GGCAAAGTTAATCCATCAATTGATGAATTTAAA
193 GGCAAAGTTAATCCAT-AATTGATGAATTTAAA
46543 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * *
46608 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAT
46673 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * ** * *
46738 AAAAGTTGATCCATTGTT-ATGGATTTGAA
195 CAAAGTTAATCCATAATTGATGAATTTAAA
* * *
46767 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * ** * *
46832 TTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
66 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAA
46896 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 TTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACT
46954 CTTCCGGAAA
Statistics
Matches: 580, Mismatches: 45, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
221 28 0.05
223 1 0.00
224 183 0.32
225 100 0.17
226 52 0.09
227 5 0.01
228 201 0.35
229 1 0.00
231 9 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (224 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
AAAGTTAATCCATAATTGATGAATTTAAA
Found at i:47470 original size:22 final size:22
Alignment explanation
Indices: 47393--47467 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
47383 TAAAGCTTTT
*
47393 ATCTTTGAAAAGAGAATCTGTC
1 ATCTTTGAAAAGAGAATCTATC
* *
47415 ATCTTTAAAAAGGGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
47437 ATCTTTGAAGAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
47459 ATCTTTGAA
1 ATCTTTGAA
47468 GAGTGTAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:47909 original size:40 final size:40
Alignment explanation
Indices: 47853--47928 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
47843 TTTCAGCTTA
47853 GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
* **
47893 GATGTAAAACATTTGACAATGCATTCATCCTTTTCT
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCT
47929 GTGGACTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
Found at i:50210 original size:114 final size:114
Alignment explanation
Indices: 50010--50436 Score: 773
Period size: 114 Copynumber: 3.7 Consensus size: 114
50000 GATCATGCAG
* * * * * *
50010 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
50075 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
50124 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
50189 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
50238 TTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
50303 ACACTTCCAGAAGATGCTATTGGGTCTTTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
50352 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
50417 ACACTTCCAGAAGATGCTAT
66 ACACTTCCAGAAGATGCTAT
50437 GAGCACATGG
Statistics
Matches: 303, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 303 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:53017 original size:2 final size:2
Alignment explanation
Indices: 53010--53061 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
53000 ACAACAAAGG
53010 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
53052 AT AT AT AT AT
1 AT AT AT AT AT
53062 GTAGAGGGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55965 original size:14 final size:14
Alignment explanation
Indices: 55945--55982 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
55935 TGCCAAATGC
55945 AAATGTAAATATGT
1 AAATGTAAATATGT
* *
55959 GAATGTAAAAATGT
1 AAATGTAAATATGT
55973 AAATGTAAAT
1 AAATGTAAAT
55983 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (14 bp):
AAATGTAAATATGT
Found at i:58384 original size:13 final size:13
Alignment explanation
Indices: 58347--58386 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
58337 TCTATATTGA
58347 AAAATAAATA-TT
1 AAAATAAATATTT
*
58359 AAAATAATTTATTT
1 AAAATAA-ATATTT
58373 AAAATAAATATTT
1 AAAATAAATATTT
58386 A
1 A
58387 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:59758 original size:14 final size:14
Alignment explanation
Indices: 59739--59777 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
59729 TTGTTATTAG
59739 GTTTGGGCCAGTCT
1 GTTTGGGCCAGTCT
59753 GTTTGGGCCAGTCT
1 GTTTGGGCCAGTCT
59767 GTTTGGGCCAG
1 GTTTGGGCCAG
59778 AACTGGGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (14 bp):
GTTTGGGCCAGTCT
Found at i:59829 original size:3 final size:3
Alignment explanation
Indices: 59821--59874 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
59811 GGCCTGGTTG
* * *
59821 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAT TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
59867 TAA TAA TA
1 TAA TAA TA
59875 TAAATAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:59838 original size:12 final size:12
Alignment explanation
Indices: 59821--59881 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
59811 GGCCTGGTTG
59821 TAATAATAATAT
1 TAATAATAATAT
59833 TAATAATAA-A-
1 TAATAATAATAT
59843 -AAT-AT-ATAT
1 TAATAATAATAT
*
59852 TAAATAAT-ATAA
1 T-AATAATAATAT
59864 TAATAATAATAT
1 TAATAATAATAT
*
59876 AAATAA
1 TAATAA
59882 AACCGGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 3 0.08
11 10 0.25
12 23 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:59880 original size:9 final size:9
Alignment explanation
Indices: 59825--59881 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
59815 TGGTTGTAAT
*
59825 AATAATATT
1 AATAATATA
*
59834 AATAATAAA
1 AATAATATA
59843 AATATATATTA
1 AATA-ATA-TA
59854 AATAATAT-
1 AATAATATA
59862 AAT-A-AT-
1 AATAATATA
59868 AATAATATA
1 AATAATATA
59877 AATAA
1 AATAA
59882 AACCGGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 5 0.12
9 17 0.43
10 6 0.15
11 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAATATA
Found at i:63133 original size:74 final size:74
Alignment explanation
Indices: 63053--63206 Score: 290
Period size: 74 Copynumber: 2.1 Consensus size: 74
63043 AGGAGTTAAC
*
63053 ACATTAAAACAAAAATAATATCCAACCGTAATATACAGTGATATATGCATCAAATTAAATCCCTA
1 ACATTAAAACAAAAATAATATCCAACCGTAATATACAATGATATATGCATCAAATTAAATCCCTA
63118 AATCATAAG
66 AATCATAAG
63127 ACATTAAAACAAAAATAATATCCAACCGTAATATACAATGATATATGCATCAAATTAAATCCCTA
1 ACATTAAAACAAAAATAATATCCAACCGTAATATACAATGATATATGCATCAAATTAAATCCCTA
63192 AATCATAAG
66 AATCATAAG
*
63201 ATATTA
1 ACATTA
63207 CAGTGTGCTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.27
Consensus pattern (74 bp):
ACATTAAAACAAAAATAATATCCAACCGTAATATACAATGATATATGCATCAAATTAAATCCCTA
AATCATAAG
Found at i:63802 original size:32 final size:32
Alignment explanation
Indices: 63761--63825 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
63751 AAAATTAAAC
63761 TTGCATGAATGCGTTTTTTTTCAAGATATCCA
1 TTGCATGAATGCGTTTTTTTTCAAGATATCCA
63793 TTGCATGAATGCGTTTTTTTTCAAGATATCCA
1 TTGCATGAATGCGTTTTTTTTCAAGATATCCA
63825 T
1 T
63826 ATTTGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (32 bp):
TTGCATGAATGCGTTTTTTTTCAAGATATCCA
Found at i:64005 original size:29 final size:29
Alignment explanation
Indices: 63973--64048 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
63963 ACAAGTTCAA
63973 CAAAAAAGTGCAATGCTACCAGCAGCAGT
1 CAAAAAAGTGCAATGCTACCAGCAGCAGT
*
64002 CAAAAAAATGCAATGCTACCAGCAGCAGT
1 CAAAAAAGTGCAATGCTACCAGCAGCAGT
64031 CAAAAAAGTGCAATGCTA
1 CAAAAAAGTGCAATGCTA
64049 AGTGAATCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.14
Consensus pattern (29 bp):
CAAAAAAGTGCAATGCTACCAGCAGCAGT
Found at i:66084 original size:4 final size:4
Alignment explanation
Indices: 66077--66177 Score: 63
Period size: 4 Copynumber: 26.2 Consensus size: 4
66067 ATAGTAAGTA
* * * *
66077 AAAT AAAT AAA- AAA- ATAT AAAA AAAT AAAG AAA- AAAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
66122 AAAAC AAAT AAAT AAA- ATAAT AAAT ATAT ATAT -AAT AAAT AAA- AACAT
1 -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT
66170 AAA- AAAT A
1 AAAT AAAT A
66178 GTATATATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
3 16 0.21
4 55 0.71
5 6 0.08
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:66096 original size:10 final size:10
Alignment explanation
Indices: 66083--66116 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
66073 AGTAAAATAA
66083 ATAAAAAAAT
1 ATAAAAAAAT
66093 ATAAAAAAAT
1 ATAAAAAAAT
*
66103 AAAGAAAAAAT
1 ATA-AAAAAAT
66114 ATA
1 ATA
66117 TAAATAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:66111 original size:13 final size:13
Alignment explanation
Indices: 66077--66166 Score: 67
Period size: 15 Copynumber: 6.7 Consensus size: 13
66067 ATAGTAAGTA
*
66077 AAATAAATAAAA-
1 AAATAAAAAAAAT
66089 AAATATAAAAAAAT
1 AAATA-AAAAAAAT
*
66103 AAAGAAAAAATATAT
1 AAATAAAAAA-A-AT
*
66118 AAATAAAACAAAT
1 AAATAAAAAAAAT
*
66131 AAAT-AAAATAAT
1 AAATAAAAAAAAT
* *
66143 AAATATATATATAAT
1 AAATA-A-AAAAAAT
66158 AAATAAAAA
1 AAATAAAAA
66167 CATAAAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
12 15 0.24
13 19 0.30
14 8 0.13
15 21 0.33
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:66153 original size:37 final size:39
Alignment explanation
Indices: 66079--66238 Score: 109
Period size: 37 Copynumber: 4.1 Consensus size: 39
66069 AGTAAGTAAA
* * *
66079 ATAAATAAAA-AAATATAAAAAAATAA-AGA-AAAAATAT
1 ATAAATAAAACAAATATAATAAAATAATA-ACATATATAT
66116 ATAAATAAAACAAATA-AATAAAATAATAA-ATATATAT
1 ATAAATAAAACAAATATAATAAAATAATAACATATATAT
* * * *
66153 AT-AATAAATAAAAACATAAAAAATAGTATATATATATATATAT
1 ATAAATAAA-ACAAATATAATAAA-A-TA-ATA-ACATATATAT
* *
66196 ATAAATTAATAAAAACAGATAATAAAA-AATAACATATATAT
1 ATAAA-TAA-AACAA-ATATAATAAAATAATAACATATATAT
66237 AT
1 AT
66239 GTAATCTAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 22
0.77 0.07 0.17
Matches are distributed among these distances:
36 6 0.06
37 33 0.33
38 11 0.11
39 1 0.01
40 2 0.02
41 14 0.14
42 4 0.04
43 11 0.11
44 2 0.02
45 8 0.08
46 9 0.09
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (39 bp):
ATAAATAAAACAAATATAATAAAATAATAACATATATAT
Found at i:66172 original size:35 final size:36
Alignment explanation
Indices: 66093--66210 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 36
66083 ATAAAAAAAT
*
66093 ATAAAA-AAATAAAGAA-A-AA-ATATATA-AATAA
1 ATAAAATAAATAAAAAATAGAATATATATATAATAA
66124 A-ACAAATAAATAAAATAATA-AATATATATATAATAA
1 ATA-AAATAAATAAAA-AATAGAATATATATATAATAA
* * *
66160 ATAAAA-ACATAAAAAATAGTATATATATAT-ATAT
1 ATAAAATAAATAAAAAATAGAATATATATATAATAA
*
66194 ATATAAATTAATAAAAA
1 ATA-AAATAAATAAAAA
66211 CAGATAATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.01
31 4 0.06
32 7 0.10
33 2 0.03
34 13 0.18
35 27 0.38
36 16 0.23
37 1 0.01
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (36 bp):
ATAAAATAAATAAAAAATAGAATATATATATAATAA
Found at i:66182 original size:27 final size:27
Alignment explanation
Indices: 66078--66182 Score: 75
Period size: 25 Copynumber: 4.0 Consensus size: 27
66068 TAGTAAGTAA
*
66078 AATAAATAAAAAAATATAA-AAA-A-AT
1 AATAAATAAAATAATA-AATAAATATAT
*
66103 AA-AGAA-AAAATATATAAATAAA-ACA-
1 AATA-AATAAAATA-ATAAATAAATATAT
*
66128 AATAAATAAAATAATAAATATATATAT
1 AATAAATAAAATAATAAATAAATATAT
66155 AATAAATAAAA-ACATAAA-AAATAGTAT
1 AATAAATAAAATA-ATAAATAAATA-TAT
66182 A
1 A
66183 TATATATATA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
24 8 0.12
25 23 0.35
26 15 0.23
27 20 0.30
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (27 bp):
AATAAATAAAATAATAAATAAATATAT
Found at i:66263 original size:43 final size:40
Alignment explanation
Indices: 66117--66264 Score: 111
Period size: 43 Copynumber: 3.5 Consensus size: 40
66107 AAAAAATATA
*
66117 TAAATAAAACAAATAAATAAAATAATAAATATATATA-TAA-
1 TAAAAAAAACAAA-AAATAAAA-AATAAATATATATATTAAT
* * * *
66157 TAAATAAAAACATAAAAAATAGTATATATATATATATATATAAAT
1 TAAA-AAAAAC--AAAAAATA--AAAAATAAATATATATATTAAT
* * *
66202 TAATAAAAACAGATAATAAAAAATAACATATATATATGTAAT
1 TAAAAAAAACAAAAAATAAAAAATAA-ATATATATAT-TAAT
*
66244 CTAAAAAAAATAAAAAATAAA
1 -TAAAAAAAACAAAAAATAAA
66265 CTAAAGTAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
40 9 0.11
41 15 0.18
42 14 0.17
43 31 0.38
44 10 0.12
45 3 0.04
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (40 bp):
TAAAAAAAACAAAAAATAAAAAATAAATATATATATTAAT
Found at i:66309 original size:23 final size:24
Alignment explanation
Indices: 66270--66315 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
66260 ATAAACTAAA
66270 GTAAAAAAGAAAATACAT-AAAAT
1 GTAAAAAAGAAAATACATGAAAAT
*
66293 GTAAAAAA-AATATTACATGAAAA
1 GTAAAAAAGAA-AATACATGAAAA
66316 AAAAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.70
24 4 0.20
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (24 bp):
GTAAAAAAGAAAATACATGAAAAT
Found at i:66841 original size:36 final size:37
Alignment explanation
Indices: 66769--66879 Score: 161
Period size: 36 Copynumber: 3.0 Consensus size: 37
66759 ATGCTTGTGG
* * *
66769 ATCCTATTTTTAAGAGTTTGAATAATAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGTAAAACTCT
66806 ATCCTATTTTTAGGAGTTTGAAT-CTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGTAAAACTCT
* * *
66842 ATCCTATTTTTAGGAGTTTGAATCCTAATAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGTAAAACTCT
66879 A
1 A
66880 ATGTTATGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 34 0.50
37 34 0.50
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATACTAGTAAAACTCT
Found at i:67507 original size:33 final size:34
Alignment explanation
Indices: 67470--67551 Score: 148
Period size: 33 Copynumber: 2.4 Consensus size: 34
67460 AAGGTCTTGG
67470 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
67503 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTGT
67538 GTTTCAAGAGAAAC
1 GTTTCAAGAGAAAC
67552 TGTCTCAAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 25 0.53
35 22 0.47
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (34 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
Found at i:67586 original size:37 final size:36
Alignment explanation
Indices: 67537--67664 Score: 110
Period size: 37 Copynumber: 3.7 Consensus size: 36
67527 GTTTTTTTTG
67537 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGGCAAAATTT
* *
67574 TGTTTCAAGAGAAACATAT-TCAA--A-G----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGGAGGCAAAATT-T
* *
67604 TGTTTCAAGAGAAACTGTCTCAAAAGAGGCAAAACTT
1 TGTTTCAAGAGAAACTGTCTC-AAGGAGGCAAAATTT
* *
67641 TGTTTCAAGGGAAATTGTCTCAAG
1 TGTTTCAAGAGAAACTGTCTCAAG
67665 AGAAACTGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
29 5 0.07
30 17 0.24
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 38 0.53
38 4 0.06
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGGCAAAATTT
Found at i:67626 original size:15 final size:15
Alignment explanation
Indices: 67608--67682 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 15
67598 GATTGGTGTT
67608 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
67623 TCAAAAGAGGCAAAACTTTGTT
1 TC--AAGA-G--AAAC--TGTC
* *
67645 TCAAGGGAAATTGTC
1 TCAAGAGAAACTGTC
67660 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
67675 TCAAGAGA
1 TCAAGAGA
67683 GACAAAACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
15 26 0.55
17 7 0.15
18 1 0.02
19 1 0.02
20 7 0.15
22 5 0.11
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:67665 original size:52 final size:52
Alignment explanation
Indices: 67608--67716 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
67598 GATTGGTGTT
* * * ** *
67608 TCAAGAGAAACTGTCTCAAAAGAGGCAAAACTTTGTTTCAAGGGAAATTGTC
1 TCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAATTATC
*
67660 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTATC
1 TCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAATTATC
67712 TCAAG
1 TCAAG
67717 GGAGACGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (52 bp):
TCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAATTATC
Found at i:67679 original size:67 final size:67
Alignment explanation
Indices: 67541--67682 Score: 162
Period size: 67 Copynumber: 2.1 Consensus size: 67
67531 TTTTTGTGTT
** * ***
67541 TCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTG
1 TCAAGAGAAACTGTCTCAAAAGAGGCAAAACTTTGTTTCAAGAGAAACATATTCAAAGATAACTG
*
67606 TT
66 TC
* * *
67608 TCAAGAGAAACTGTCTCAAAAGAGGCAAAACTTTGTTTCAAGGGAAA-TTGTCTCAAGAGA-AAC
1 TCAAGAGAAACTGTCTCAAAAGAGGCAAAACTTTGTTTCAAGAGAAACATAT-TCAA-AGATAAC
67671 TGTC
64 TGTC
67675 TCAAGAGA
1 TCAAGAGA
67683 GACAAAACTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 2 0.03
67 58 0.92
68 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (67 bp):
TCAAGAGAAACTGTCTCAAAAGAGGCAAAACTTTGTTTCAAGAGAAACATATTCAAAGATAACTG
TC
Found at i:67836 original size:102 final size:103
Alignment explanation
Indices: 67655--67845 Score: 251
Period size: 102 Copynumber: 1.9 Consensus size: 103
67645 TCAAGGGAAA
* *
67655 TTGTCTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTATCTCAAGGGA
1 TTGTCTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGA
*
67720 GACGAAATTTGTTTCAA-GGAAAACATATTCAAAGATT
66 GACAAAATTTGTTTCAAGGGAAAACATATTCAAAGATT
* * * * ** * *
67757 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTTAAGAGA
1 TTGTCTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGA
*
67821 GATAAAACTTTGTTTCAAGGGAAAA
66 GACAAAA-TTTGTTTCAAGGGAAAA
67846 TGTCTCAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
101 26 0.35
102 43 0.57
103 6 0.08
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (103 bp):
TTGTCTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGA
GACAAAATTTGTTTCAAGGGAAAACATATTCAAAGATT
Found at i:67842 original size:37 final size:37
Alignment explanation
Indices: 67756--67872 Score: 200
Period size: 37 Copynumber: 3.2 Consensus size: 37
67746 ATTCAAAGAT
67756 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
* *
67792 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGATAAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
*
67829 TTTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
67866 TTTGTTT
1 TTTGTTT
67873 TGAGTAAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 34 0.45
37 41 0.55
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
Found at i:68552 original size:32 final size:31
Alignment explanation
Indices: 68479--68557 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
68469 TCGCATCAGG
* * * *
68479 ATGTTGAATCCCCAAAGATACCCCAATATTC
1 ATGTTGAATCTCCAAAAATACCCCAACATTA
*
68510 GTGTTGAATCTCCAAAAATACCCCAACATTTA
1 ATGTTGAATCTCCAAAAATACCCCAACA-TTA
*
68542 ATGTTGAATCTTCAAA
1 ATGTTGAATCTCCAAA
68558 GATTCCCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.60
32 16 0.40
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (31 bp):
ATGTTGAATCTCCAAAAATACCCCAACATTA
Found at i:70150 original size:21 final size:21
Alignment explanation
Indices: 70126--70179 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
70116 CTCGGAGGGA
70126 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
70147 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
70168 ACCGATTCCCCC
1 ACCGATTCCCCC
70180 CTGTTCAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.39, G:0.24, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCCATAGGGGGT
Done.