Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:272386 original size:16 final size:15
Alignment explanation
Indices: 272343--272386 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
272333 ATTTTTAAAT
272343 AAATTTTATTAATTA
1 AAATTTTATTAATTA
*
272358 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATT-A
272375 AAATTTTATTAA
1 AAATTTTATTAA
272387 AACCTCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTTATTAATTA
Found at i:275732 original size:2 final size:2
Alignment explanation
Indices: 275725--275756 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
275715 AAATTCTTAA
275725 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
275757 GGATTTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276618 original size:18 final size:18
Alignment explanation
Indices: 276580--276636 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
276570 CCGACCCTTG
*
276580 TTCTATATTTT-TTTC-A
1 TTCTTTATTTTCTTTCTA
*
276596 TTCTTTTTTTTCTTTCTA
1 TTCTTTATTTTCTTTCTA
* *
276614 TTCTTTATTTTCCTTCTT
1 TTCTTTATTTTCTTTCTA
276632 TTCTT
1 TTCTT
276637 GGCCTAACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 21 0.62
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTTATTTTCTTTCTA
Found at i:277128 original size:17 final size:17
Alignment explanation
Indices: 277095--277130 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
277085 TTTTAATTCA
**
277095 AAAAAAATATATTTAAT
1 AAAAAAATATAAATAAT
277112 AAAAAAATATAAATAAT
1 AAAAAAATATAAATAAT
277129 AA
1 AA
277131 TTAAATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAAATATAAATAAT
Found at i:277261 original size:15 final size:14
Alignment explanation
Indices: 277211--277265 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
277201 TTTATTTTTT
277211 TAATTTAAATATTTA
1 TAATTTAAA-ATTTA
*
277226 TAATTTAAAA-TAA
1 TAATTTAAAATTTA
*
277239 T-TTTTAAAATGTTA
1 TAATTTAAAAT-TTA
277253 TAATTTAAAATTT
1 TAATTTAAAATTT
277266 TGCTTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 6 0.18
15 17 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TAATTTAAAATTTA
Found at i:278909 original size:1 final size:1
Alignment explanation
Indices: 278905--278929 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
278895 ATTAAAAAGT
278905 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
278930 CACTTAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:281839 original size:6 final size:6
Alignment explanation
Indices: 281828--281855 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
281818 CCCTATTTCT
281828 CTTTTA CTTTTA CTTTTA CTTTTA CTTT
1 CTTTTA CTTTTA CTTTTA CTTTTA CTTT
281856 GCTTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
CTTTTA
Found at i:282146 original size:17 final size:17
Alignment explanation
Indices: 282124--282167 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
282114 AATCATTTTA
282124 ATTAAATAAAATTTAA-T
1 ATTAAATAAAA-TTAATT
282141 ATTAAAT-AAATTAATT
1 ATTAAATAAAATTAATT
*
282157 AATAAATAAAA
1 ATTAAATAAAA
282168 ATATGTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAAATAAAATTAATT
Found at i:289540 original size:2 final size:2
Alignment explanation
Indices: 289533--289566 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
289523 AAAGTTTTCT
289533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
289567 AAATTATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:292776 original size:21 final size:19
Alignment explanation
Indices: 292752--292810 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
292742 TTTTATAATT
*
292752 TAAAATTCATATTTATCTTAA
1 TAAAATT-ATATTCATC-TAA
292773 T-AAATTATATTCATCTAA
1 TAAAATTATATTCATCTAA
292791 T-AAA-TATAATT-ATCTAA
1 TAAAATTAT-ATTCATCTAA
292808 TAA
1 TAA
292811 TTATAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 10 0.29
18 11 0.31
19 8 0.23
20 5 0.14
21 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTATATTCATCTAA
Found at i:292788 original size:19 final size:17
Alignment explanation
Indices: 292754--292815 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
292744 TTATAATTTA
292754 AAATTCATATTTATCTTAAT
1 AAATT-ATA-TTATC-TAAT
292774 AAATTATATTCATCTAAT
1 AAATTATATT-ATCTAAT
292792 AAA-TATAATTATCTAAT
1 AAATTAT-ATTATCTAAT
292809 -AATTATA
1 AAATTATA
292816 AAATTAGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.08
17 13 0.33
18 12 0.31
19 6 0.15
20 5 0.13
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTATATTATCTAAT
Found at i:293025 original size:25 final size:25
Alignment explanation
Indices: 292997--293048 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
292987 AAGACGTAAG
292997 ATAGAAAAATTTGATTCATAATCAA
1 ATAGAAAAATTTGATTCATAATCAA
*
293022 ATAGAAAAATTTTATTCATAATCAA
1 ATAGAAAAATTTGATTCATAATCAA
293047 AT
1 AT
293049 CTCTAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (25 bp):
ATAGAAAAATTTGATTCATAATCAA
Found at i:300369 original size:15 final size:13
Alignment explanation
Indices: 300335--300360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300325 AAATTAAATT
300335 TTATATATTTAAA
1 TTATATATTTAAA
300348 TTATATATTTAAA
1 TTATATATTTAAA
300361 ATTAGTATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATATATTTAAA
Found at i:301230 original size:20 final size:20
Alignment explanation
Indices: 301205--301301 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
301195 TTTTACCCAG
301205 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
301225 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
301245 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
301265 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
301285 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
301302 ATCTTTTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:301242 original size:12 final size:12
Alignment explanation
Indices: 301225--301278 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
301215 ACATTTTTCA
301225 ATGTATCGATAC
1 ATGTATCGATAC
301237 ATGTAT-G--A-
1 ATGTATCGATAC
301245 ATGTATCGATAC
1 ATGTATCGATAC
301257 ATGTAT-G--A-
1 ATGTATCGATAC
301265 ATGTATCGATAC
1 ATGTATCGATAC
301277 AT
1 AT
301279 TCTTCAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
11 4 0.12
12 14 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:315234 original size:16 final size:15
Alignment explanation
Indices: 315208--315266 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
315198 TCGTACCAAA
315208 AAAATAAAAAAAACAT
1 AAAA-AAAAAAAACAT
315224 AAAAAACAAAAAA-AT
1 AAAAAA-AAAAAACAT
* *
315239 TAAACAAAAAAACA-
1 AAAAAAAAAAAACAT
315253 AACAAATAAAAAAA
1 AA-AAA-AAAAAAA
315267 GAGGTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.20
15 11 0.31
16 17 0.49
ACGTcount: A:0.83, C:0.08, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAAAAAAAAAACAT
Found at i:315237 original size:21 final size:20
Alignment explanation
Indices: 315213--315264 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
315203 CCAAAAAAAT
315213 AAAAAAAACATAAAAAACAAA
1 AAAAAAAACA-AAAAAACAAA
*
315234 AAAATTAAACAAAAAAACAAA
1 AAAA-AAAACAAAAAAACAAA
315255 CAAATAAAAA
1 -AAA-AAAAA
315265 AAGAGGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 14 0.54
22 11 0.42
23 1 0.04
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAAAAAACAAAAAAACAAA
Found at i:316529 original size:29 final size:27
Alignment explanation
Indices: 316476--316836 Score: 344
Period size: 28 Copynumber: 12.7 Consensus size: 27
316466 CTAGAACGTT
* **
316476 CATCTCTTCAAAACCCACTGGTCAGTGG
1 CATC-CTTCAAAGCCCACAAGTCAGTGG
***
316504 CATCTCTTCAAAAAAACACAAGTCAGTGG
1 CATC-CTTC-AAAGCCCACAAGTCAGTGG
**
316533 CATCTCTTCAAAAAACCACAAGTCAGTGG
1 CATC-CTTC-AAAGCCCACAAGTCAGTGG
*
316562 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
*
316590 CATCCTTCTTAAAGCCCACAAGTTAGTGG
1 CATCCTTC--AAAGCCCACAAGTCAGTGG
**
316619 CATTTTTTCAAAGCCCACAAGTCAGTGG
1 CA-TCCTTCAAAGCCCACAAGTCAGTGG
316647 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
*
316675 CATCCTTTCAAAGCCCACAAGTAAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
* * * *
316703 CACCCTTTTAAAGCCCATAGGTCAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
* *
316731 CATCCTTTCAAAGCCCATAAGTTAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
* *
316759 CATCCTTTCAAAGCCCATAAGTTAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
* * *
316787 TACCCTTTCAAAACCCACAAGTCAGTGG
1 CATCC-TTCAAAGCCCACAAGTCAGTGG
*
316815 CACCCTTTTCAAAGCCCACAAG
1 CATCC--TTCAAAGCCCACAAG
316837 CTAATGGTAA
Statistics
Matches: 296, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
27 4 0.01
28 202 0.68
29 86 0.29
30 4 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (27 bp):
CATCCTTCAAAGCCCACAAGTCAGTGG
Found at i:316686 original size:56 final size:56
Alignment explanation
Indices: 316520--316943 Score: 415
Period size: 56 Copynumber: 7.4 Consensus size: 56
316510 TTCAAAAAAA
**
316520 CACAAGTCAGTGGCAT-CTCTTCAAAAAACCACAAGTCAGTGGCATCCTTTCAAAGCC
1 CACAAGTCAGTGGCATCCT-TTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * **
316577 CACAAGTTAGTGGCATCCTTCTTAAAGCCCACAAGTTAGTGGCATTTTTTCAAAGCC
1 CACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
316634 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
1 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * * *
316690 CACAAGTAAGTGGCACCCTTTTAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCC
1 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * * * * *
316746 CATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGTACCCTTTCAAAACC
1 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * *
316802 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAG-CTAATGGTAACTCTTTTCAAAGCC
1 CACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTC-AGTGG-CA-TCCTTTCAAAGCC
* * * * * *
316861 CATAAGTCAGTGGTAACTCTTTTTAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGTCC
1 CACAAGTCAGTGG-CA-TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC
*
316924 ACACAAGTTAGT-GCA-CCTTT
1 -CACAAGTCAGTGGCATCCTTT
316944 TTTTAAAAGC
Statistics
Matches: 305, Mismatches: 48, Indels: 25
0.81 0.13 0.07
Matches are distributed among these distances:
56 145 0.48
57 83 0.27
58 4 0.01
59 22 0.07
60 12 0.04
61 3 0.01
62 23 0.08
63 4 0.01
64 9 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (56 bp):
CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
Found at i:316741 original size:84 final size:84
Alignment explanation
Indices: 316548--316943 Score: 447
Period size: 84 Copynumber: 4.6 Consensus size: 84
316538 CTTCAAAAAA
*
316548 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTCTTAAAGCCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTT-TCAAAGCCCACAAGT
**
316613 TAGTGGCA-TTTTTTCAAAGC
65 TAGTGGCACCCTTTT-AAAGC
* *
316633 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTA
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
316698 AGTGGCACCCTTTTAAAGC
66 AGTGGCACCCTTTTAAAGC
* * * *
316717 CCATAGGTCAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
* * *
316782 AGTGGTACCCTTTCAAAAC
66 AGTGGCACCCTTTTAAAGC
* * * * * *
316801 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGCTAATGGTAACTCTTTTCAAAGCCCATAA
1 CCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGG-CA-TCCTTTCAAAGCCCACAA
* * *
316866 GTCAGTGGTAACTCTTTTTAAAGCC
63 GTTAGTGG-CAC-CCTTTTAAAG-C
* *
316891 CACACAAGTCGGTGGCAACTCTTTTCAAAGTCCACACAAGTTAGT-GCA-CCTTT
1 C-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CACAAGTTAGTGGCATCCTTT
316944 TTTTAAAAGC
Statistics
Matches: 265, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
84 117 0.44
85 72 0.27
86 1 0.00
87 24 0.09
88 2 0.01
89 7 0.03
90 6 0.02
91 13 0.05
92 10 0.04
93 4 0.02
94 9 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (84 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
AGTGGCACCCTTTTAAAGC
Found at i:316855 original size:30 final size:30
Alignment explanation
Indices: 316548--316936 Score: 269
Period size: 28 Copynumber: 13.4 Consensus size: 30
316538 CTTCAAAAAA
* *
316548 CCACAAGTCAGTGG-CA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* * *
316576 CCACAAGTTAGTGGCATC-CTTCTT-AAAGC
1 CCACAAGTCAGTGGTAACTCTT-TTCAAAGC
* * *
316605 CCACAAGTTAGTGG-CA-TTTTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* *
316633 CCACAAGTCAGTGG-CA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* *
316661 CCACAAGTCAGTGG-CA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* * *
316689 CCACAAGTAAGTGG-CACCCTTTT-AAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* * * *
316717 CCATAGGTCAGTGG-CA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* * * *
316745 CCATAAGTTAGTGG-CA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* * * *
316773 CCATAAGTTAGTGGT-AC-CCTTTCAAAAC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
* *
316801 CCACAAGTCAGTGG-CACCCTTTTCAAAGC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAGC
*
316830 CCACAAG-CTAATGGTAACTCTTTTCAAAGC
1 CCACAAGTC-AGTGGTAACTCTTTTCAAAGC
* *
316860 CCATAAGTCAGTGGTAACTCTTTTTAAAGCC
1 CCACAAGTCAGTGGTAACTCTTTTCAAAG-C
* *
316891 CACACAAGTCGGTGGCAACTCTTTTCAAAGTC
1 C-CACAAGTCAGTGGTAACTCTTTTCAAAG-C
*
316923 CACACAAGTTAGTG
1 C-CACAAGTCAGTG
316937 CACCTTTTTT
Statistics
Matches: 307, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.02
28 177 0.58
29 45 0.15
30 39 0.13
31 3 0.01
32 37 0.12
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (30 bp):
CCACAAGTCAGTGGTAACTCTTTTCAAAGC
Found at i:316911 original size:32 final size:32
Alignment explanation
Indices: 316549--316983 Score: 164
Period size: 28 Copynumber: 14.8 Consensus size: 32
316539 TTCAAAAAAC
* *
316549 CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * *
316577 CACAAGTTAGTGGCATC-CTTCTTAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
*
316606 CACAAGTTAGTGGC-A-T-TTTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTT-AAAGCCCA
* *
316634 CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* *
316662 CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* *
316690 CACAAGTAAGTGGC-AC-CCTTTTAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * * *
316718 CATAGGTCAGTGGC-A-TCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * * *
316746 CATAAGTTAGTGGC-A-TCCTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * * * * *
316774 CATAAGTTAGTGG-TAC-CCTTTCAAA-ACC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* *
316802 CACAAGTCAGTGGC-ACCCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * *
316831 CACAAG-CTAATGGTAACTCTTTTCAAAG-CC-
1 CACAAGTC-AGTGGCAACTCTTTTTAAAGCCCA
* *
316861 CATAAGTCAGTGGTAACTCTTTTTAAAGCCCA
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * *
316893 CACAAGTCGGTGGCAACTCTTTTCAAAGTCCA
1 CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
* * * *
316925 CACAAGTTAGT-GCACCTTTTTTTAAAAGCCTA
1 CACAAGTCAGTGGCAACTCTTTTT-AAAGCCCA
* *
316957 CGCAAGTCGGTGGCAACTCTTTTTAAA
1 CACAAGTCAGTGGCAACTCTTTTTAAA
316984 TCACCACTTT
Statistics
Matches: 343, Mismatches: 44, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.01
28 181 0.53
29 46 0.13
30 37 0.11
31 12 0.03
32 53 0.15
33 10 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (32 bp):
CACAAGTCAGTGGCAACTCTTTTTAAAGCCCA
Found at i:317478 original size:215 final size:215
Alignment explanation
Indices: 317107--317528 Score: 790
Period size: 215 Copynumber: 2.0 Consensus size: 215
317097 TTAGCCCAAT
*
317107 GTCGCTGGCCTTGAATTGGCACATTGGTACTCCTCTTATCTCTAAGTCTAGTGTTGTAGGCCTTG
1 GTCGCTGGCCTTGAATTGGCACATTGGCACTCCTCTTATCTCTAAGTCTAGTGTTGTAGGCCTTG
*
317172 AATCTGCACATGGGCACATCACGGACACTGATCATGCCCTCACCAATCTTCAAGGAGTCATATCC
66 AATCTGCACATGGGCACATCACGGACACTGATCATGCCCTCACCAATCCTCAAGGAGTCATATCC
317237 TTCCACAACACCTGTCTAATTCTACCCCGAACGTGTCTATTTGTCTTTACCCTATTGTTGATACT
131 TTCCACAACACCTGTCTAATTCTACCCCGAACGTGTCTATTTGTCTTTACCCTATTGTTGATACT
317302 CAACAATGACCACAACACCC
196 CAACAATGACCACAACACCC
*
317322 GTCGCTGGCCTTGAATTGGCACATTGGCACTCTTCTTATCTCTAAGTCTAGTGTTGTAGGCCTTG
1 GTCGCTGGCCTTGAATTGGCACATTGGCACTCCTCTTATCTCTAAGTCTAGTGTTGTAGGCCTTG
*
317387 AATCTGCACATGGGCACATCACGGACACTGATCATGCCCTCATCAATCCTCAAGGAGTCATATCC
66 AATCTGCACATGGGCACATCACGGACACTGATCATGCCCTCACCAATCCTCAAGGAGTCATATCC
* *
317452 TTCCACAACACCTGTCTAATTCTACCCTGAACGTGTCTATTTGTCTTTACCCTGTTGTTGATACT
131 TTCCACAACACCTGTCTAATTCTACCCCGAACGTGTCTATTTGTCTTTACCCTATTGTTGATACT
317517 CAACAATGACCA
196 CAACAATGACCA
317529 AAGAGGGGCA
Statistics
Matches: 201, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
215 201 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (215 bp):
GTCGCTGGCCTTGAATTGGCACATTGGCACTCCTCTTATCTCTAAGTCTAGTGTTGTAGGCCTTG
AATCTGCACATGGGCACATCACGGACACTGATCATGCCCTCACCAATCCTCAAGGAGTCATATCC
TTCCACAACACCTGTCTAATTCTACCCCGAACGTGTCTATTTGTCTTTACCCTATTGTTGATACT
CAACAATGACCACAACACCC
Found at i:318079 original size:20 final size:20
Alignment explanation
Indices: 318054--318182 Score: 89
Period size: 20 Copynumber: 5.9 Consensus size: 20
318044 TGTACGTATG
318054 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
318074 AATGTATCGATACATTCTGTCTTTTTACTC
1 AATGTATCGATACA---T-TC----T--TC
* *
318104 AGATGTATTGATACATTTTTC
1 A-ATGTATCGATACATTCTTC
* *
318125 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
*
318145 AATGTATAGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
318165 AATGTATCGATATATTCT
1 AATGTATCGATACATTCT
318183 GTCTTTTTAC
Statistics
Matches: 86, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
19 1 0.01
20 59 0.69
21 4 0.05
23 2 0.02
24 2 0.02
27 1 0.01
28 2 0.02
30 3 0.03
31 12 0.14
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:318117 original size:51 final size:50
Alignment explanation
Indices: 318054--318223 Score: 180
Period size: 51 Copynumber: 3.6 Consensus size: 50
318044 TGTACGTATG
318054 AATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTC
1 AATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTC
* * *
318104 AGATGTATTGATACATTTTTCAATGTATCGATACA---TG------TA-TG
1 A-ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTC
* * *
318145 AATGTATAGATACATTCTTCAATGTATCGATATATTCTGTCTTTTTACCC
1 AATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTC
* *
318195 AAATGTATCGATACATTATTTAATGTATC
1 -AATGTATCGATACATTCTTCAATGTATC
318224 AACACATCTA
Statistics
Matches: 97, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
40 30 0.31
41 2 0.02
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 1 0.01
51 56 0.58
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (50 bp):
AATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTC
Found at i:318208 original size:91 final size:91
Alignment explanation
Indices: 318049--318223 Score: 289
Period size: 91 Copynumber: 1.9 Consensus size: 91
318039 CCAGATGTAC
* * * *
318049 GTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACTCAGATGTATTG
1 GTATGAATGTATAGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCG
318114 ATACATT-TTTCAATGTATCGATACAT
66 ATACATTATTT-AATGTATCGATACAT
*
318140 GTATGAATGTATAGATACATTCTTCAATGTATCGATATATTCTGTCTTTTTACCCAAATGTATCG
1 GTATGAATGTATAGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCG
318205 ATACATTATTTAATGTATC
66 ATACATTATTTAATGTATC
318224 AACACATCTA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 75 0.96
92 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (91 bp):
GTATGAATGTATAGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATCG
ATACATTATTTAATGTATCGATACAT
Found at i:322351 original size:21 final size:19
Alignment explanation
Indices: 322311--322353 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
322301 TAAAAAAGTT
322311 AAAATTAAAAAATATAATA
1 AAAATTAAAAAATATAATA
322330 AAAATTAAAAAATATAATA
1 AAAATTAAAAAATATAATA
*
322349 TAAAT
1 AAAAT
322354 GGATGCGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTAAAAAATATAATA
Found at i:323353 original size:27 final size:26
Alignment explanation
Indices: 323304--323380 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
323294 CATTTCTCTC
*
323304 CTCTCTCTTTCATTTTC-CGTCTTTCCTT
1 CTCT-TCTTTCTTTTTCTC-TCTTT-CTT
*
323332 CTCTTCTTTCTTTTTCTCTCTTTTTT
1 CTCTTCTTTCTTTTTCTCTCTTTCTT
*
323358 CTCTCCATTTCCTTCTTTCTCTC
1 CTCTTC-TTT-CTT-TTTCTCTC
323381 CTAAAACTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.17
27 19 0.45
28 8 0.19
29 8 0.19
ACGTcount: A:0.03, C:0.35, G:0.01, T:0.61
Consensus pattern (26 bp):
CTCTTCTTTCTTTTTCTCTCTTTCTT
Found at i:325892 original size:1 final size:1
Alignment explanation
Indices: 325886--325955 Score: 77
Period size: 1 Copynumber: 70.0 Consensus size: 1
325876 AAATCTTCAC
* * * * * * *
325886 TTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTTCTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
325951 TTTTT
1 TTTTT
325956 CCAATTGCCA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:325902 original size:11 final size:11
Alignment explanation
Indices: 325886--325949 Score: 92
Period size: 11 Copynumber: 5.6 Consensus size: 11
325876 AAATCTTCAC
325886 TTTTTTTTTTG
1 TTTTTTTTTTG
325897 TTTTTTTTTTG
1 TTTTTTTTTTG
*
325908 TTTTTTTTTTC
1 TTTTTTTTTTG
*
325919 TTTTTTTTTGTT
1 TTTTTTTTT-TG
325931 TTTTTTGTTTTG
1 TTTTTT-TTTTG
325943 TTTTTTT
1 TTTTTTT
325950 CTTTTTCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
11 31 0.65
12 14 0.29
13 3 0.06
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:325913 original size:21 final size:21
Alignment explanation
Indices: 325887--325948 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
325877 AATCTTCACT
325887 TTTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTTGTTTTTTTTTTG
325908 TTTTTTTTT-TCTTTTTTTTTG
1 TTTTTTTTTGT-TTTTTTTTTG
325929 -TTTTTTTTGTTTTGTTTTTT
1 TTTTTTTTTGTTTT-TTTTTT
325949 TCTTTTTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.32
21 26 0.68
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (21 bp):
TTTTTTTTTGTTTTTTTTTTG
Found at i:325927 original size:32 final size:32
Alignment explanation
Indices: 325887--325955 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
325877 AATCTTCACT
*
325887 TTTTTTTTTGTTTTTTTT-TTGTTTTTTTTTTC
1 TTTTTTTTTGTTTTTTTTGTT-TTGTTTTTTTC
325919 TTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTC
1 TTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTC
325951 TTTTT
1 TTTTT
325956 CCAATTGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (32 bp):
TTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTC
Found at i:325954 original size:21 final size:19
Alignment explanation
Indices: 325886--325955 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 19
325876 AAATCTTCAC
325886 TTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTGTTTTTTTT
*
325905 TTGTTTTTTTTTTCTTTTTTT
1 TT-TTTTTTTTGT-TTTTTTT
325926 TTGTTTTTTTTGTTTTGTTTT
1 TT-TTTTTTTTGTTTT-TTTT
325947 TTTCTTTTT
1 TTT-TTTTT
325956 CCAATTGCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 30 0.67
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTTTTT
Found at i:337824 original size:4 final size:4
Alignment explanation
Indices: 337815--337839 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
337805 AACTTTAACA
337815 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
337840 CTTAAGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:342072 original size:14 final size:14
Alignment explanation
Indices: 342050--342079 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
342040 AAATATTTAA
*
342050 AATTTATTTAATTT
1 AATTAATTTAATTT
342064 AATTAATTTAATTT
1 AATTAATTTAATTT
342078 AA
1 AA
342080 ATTGAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTAATTTAATTT
Found at i:342558 original size:15 final size:14
Alignment explanation
Indices: 342534--342575 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
342524 TCCGAGGACC
342534 TTTTTGTTTTATAAA
1 TTTTT-TTTTATAAA
342549 TTTTATTTTTAT-AA
1 TTTT-TTTTTATAAA
342563 TTTTTTATTTATA
1 TTTTTT-TTTATA
342576 TTATTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 11 0.46
15 10 0.42
16 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTATAAA
Found at i:342752 original size:27 final size:28
Alignment explanation
Indices: 342670--342761 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 28
342660 ATTTAATAAG
*
342670 TTTAT-TTATTCATATCATATTTATATT-
1 TTTATATTA-TCATATTATATTTATATTA
* * *
342697 TTTATATTATCATATTTTAATTATTTTA
1 TTTATATTATCATATTATATTTATATTA
342725 TTT-TATTAT-ATAATTATATTTATATTA
1 TTTATATTATCAT-ATTATATTTATATTA
*
342752 TAATATATTA
1 T-TTATATTA
342762 AAACATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.04
27 38 0.73
28 7 0.13
29 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATATTATCATATTATATTTATATTA
Found at i:343305 original size:20 final size:20
Alignment explanation
Indices: 343282--343335 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
343272 CACACCCAGA
343282 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
343302 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
343322 TGTATCGATACATT
1 TGTATCGATACATT
343336 GTATTGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:343434 original size:13 final size:13
Alignment explanation
Indices: 343416--343440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343406 TACATGGTAC
343416 ATTGTATCGATAT
1 ATTGTATCGATAT
343429 ATTGTATCGATA
1 ATTGTATCGATA
343441 CATGATGAAT
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:343441 original size:33 final size:33
Alignment explanation
Indices: 343397--343465 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
343387 CTACCATTAT
* * *
343397 TTGTATTGATACATGGT-ACATTGTATCGATATA
1 TTGTATCGATACATGATGA-ATTGTATAGATATA
343430 TTGTATCGATACATGATGAATTGTATAGATATA
1 TTGTATCGATACATGATGAATTGTATAGATATA
343463 TTG
1 TTG
343466 CTTCAAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATAGATATA
Found at i:351370 original size:13 final size:13
Alignment explanation
Indices: 351352--351376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351342 CATTATGCTT
351352 TGTATCGATACAA
1 TGTATCGATACAA
351365 TGTATCGATACA
1 TGTATCGATACA
351377 TGTTCATTAT
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:351411 original size:20 final size:20
Alignment explanation
Indices: 351361--351415 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
351351 TTGTATCGAT
*
351361 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
351380 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
351399 ACAATTGTATCGATACA
1 ACAATTGTATCGATACA
351416 AGAAACTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:351471 original size:20 final size:20
Alignment explanation
Indices: 351446--351499 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
351436 CTACCACTGT
* *
351446 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
351466 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
*
351486 TTATATCGATACAT
1 TTGTATCGATACAT
351500 TGCTTCAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:354327 original size:271 final size:271
Alignment explanation
Indices: 353843--354332 Score: 619
Period size: 271 Copynumber: 1.8 Consensus size: 271
353833 GGTATGAATT
* * * *
353843 TTGTTAGGATCAAGTGCTTACGATTAGGCCAAAAGCTATAGCTATTAATCAGGGCGCAACTTTAT
1 TTGTTAGGATCAAGCGCTTACCATTAGGCCAAAAGCTATAACTATTAATCAGGGCACAACTTTAT
* * * * *
353908 TTCTTAACTCATGACAGCTCAAAGCCTCGTGCTATGCGACAAGAAGACATGAGGGGTTGCACCCA
66 TTCTTAACTCATGACAGCTCAAAGCCCCGTGCTAAGCGACAAGAAGACATGAGGAGCTACACCCA
* ** * * *
353973 TATGGGTGCCGCAGGTCCGGTGGTTAGTCCACGACCAATTACGTTCTCCCGAGTCAAAGGATGGT
131 CATGACTACCGCAGGTCAGGCGGTTAGTCCACGACCAATTACGTTCTCCCGAGTCAAAGGATGGT
* **
354038 GCTGACCCTCTTTAAGGTCAACAATCACCCCCCCAATACTAGCCTAGGAGACTTGAACCTATGAC
196 GCTGACCCCCCATAAGGTCAACAATCACCCCCCCAATACTAGCCTAGGAGACTTGAACCTATGAC
354103 TCTGATACCAA
261 TCTGATACCAA
* * * *
354114 TTGTTAGGATCGAGCG-TATACCATTAGGCCAAAAGCTATAACTATTAGTTAGGGCATAACTTTA
1 TTGTTAGGATCAAGCGCT-TACCATTAGGCCAAAAGCTATAACTATTAATCAGGGCACAACTTTA
* * * * **
354178 TTTCTTAACTTATGGCAG-TGCAGAGCCCCGTGCTAAGCGACAGGTGGACATGAGGAGCTACACC
65 TTTCTTAACTCATGACAGCT-CAAAGCCCCGTGCTAAGCGACAAGAAGACATGAGGAGCTACACC
* * * * *
354242 CACGTGACTACCGTAGGTCAGGCGGTTAGTCCAC-AGCTAGTTACGTTCTCTCGAGTCAAAGG-T
129 CACATGACTACCGCAGGTCAGGCGGTTAGTCCACGA-CCAATTACGTTCTCCCGAGTCAAAGGAT
354305 GGTGCTGACCCCCCCATAAGGTCAACAA
193 GGTGCTGA-CCCCCCATAAGGTCAACAA
354333 ATTTTAAATC
Statistics
Matches: 182, Mismatches: 33, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
270 12 0.07
271 170 0.93
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (271 bp):
TTGTTAGGATCAAGCGCTTACCATTAGGCCAAAAGCTATAACTATTAATCAGGGCACAACTTTAT
TTCTTAACTCATGACAGCTCAAAGCCCCGTGCTAAGCGACAAGAAGACATGAGGAGCTACACCCA
CATGACTACCGCAGGTCAGGCGGTTAGTCCACGACCAATTACGTTCTCCCGAGTCAAAGGATGGT
GCTGACCCCCCATAAGGTCAACAATCACCCCCCCAATACTAGCCTAGGAGACTTGAACCTATGAC
TCTGATACCAA
Found at i:358963 original size:30 final size:32
Alignment explanation
Indices: 358928--358991 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
358918 AATAAAAATA
*
358928 AATCATACTT-TAAA-AAATTTAAACTTGTAT
1 AATCATACTTAAAAATAAATTTAAACTTGTAT
* *
358958 AATCATACTTAAAAATAAATTTAAATTTTTAT
1 AATCATACTTAAAAATAAATTTAAACTTGTAT
358990 AA
1 AA
358992 ATAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 10 0.34
31 3 0.10
32 16 0.55
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (32 bp):
AATCATACTTAAAAATAAATTTAAACTTGTAT
Found at i:358988 original size:73 final size:72
Alignment explanation
Indices: 358842--359033 Score: 289
Period size: 73 Copynumber: 2.7 Consensus size: 72
358832 TAAATTAATC
*
358842 TTATAAATAAAAATAAATCATA-TTTAAAAAAATTAAACTCGTATAATCAAACTAAAAATAAATT
1 TTATAAATAAAAATAAATCATACTTTAAAAAATTTAAACTCGTATAATCAAACTAAAAATAAATT
358906 TAAACTT
66 TAAACTT
* *
358913 TTATAAATAAAAATAAATCATACTTTAAAAAATTTAAACTTGTATAATCATACTTAAAAATAAAT
1 TTATAAATAAAAATAAATCATACTTTAAAAAATTTAAACTCGTATAATCAAAC-TAAAAATAAAT
*
358978 TTAAATTT
65 TTAAACTT
* * * *
358986 TTATAAATAAAAATAAATTATACATTAAAAAA-TTAAGCTCGTGTAATC
1 TTATAAATAAAAATAAATCATACTTTAAAAAATTTAAACTCGTATAATC
359034 CTTTGAAACT
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
71 22 0.20
72 40 0.36
73 48 0.44
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (72 bp):
TTATAAATAAAAATAAATCATACTTTAAAAAATTTAAACTCGTATAATCAAACTAAAAATAAATT
TAAACTT
Found at i:360891 original size:20 final size:19
Alignment explanation
Indices: 360863--360937 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
360853 TCATACCCTG
*
360863 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
360883 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
*
360903 ATGTATCGATATATTCTATA
1 ATGTATCGATACATT-TATA
360923 ATGTATCGATACATT
1 ATGTATCGATACATT
360938 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:360930 original size:40 final size:39
Alignment explanation
Indices: 360863--360940 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
360853 TCATACCCTG
*
360863 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCGATACAT-TATGA
* *
360903 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCGATACATTATG
360941 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCGATACATTATGA
Found at i:374959 original size:8 final size:8
Alignment explanation
Indices: 374946--375005 Score: 72
Period size: 8 Copynumber: 7.6 Consensus size: 8
374936 CTTTACACCC
374946 AAAAACAA
1 AAAAACAA
374954 AAAAACAA
1 AAAAACAA
374962 AAAAGTA-AA
1 AAAA--ACAA
374971 AAAAACAA
1 AAAAACAA
374979 AAAAA-AA
1 AAAAACAA
*
374986 TAAAAC-A
1 AAAAACAA
374993 AAAAACAA
1 AAAAACAA
375001 AAAAA
1 AAAAA
375006 AAGAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
7 13 0.29
8 25 0.56
9 6 0.13
10 1 0.02
ACGTcount: A:0.87, C:0.08, G:0.02, T:0.03
Consensus pattern (8 bp):
AAAAACAA
Found at i:374974 original size:17 final size:15
Alignment explanation
Indices: 374946--375015 Score: 79
Period size: 15 Copynumber: 4.5 Consensus size: 15
374936 CTTTACACCC
*
374946 AAAAACAAAAAAACA
1 AAAAAAAAAAAAACA
374961 AAAAAGTAAAAAAAACA
1 AAAAA--AAAAAAAACA
*
374978 AAAAAAAATAAAACA
1 AAAAAAAAAAAAACA
374993 AAAAACAAAAAAAA-A
1 AAAAA-AAAAAAAACA
375008 GAAAAAAA
1 -AAAAAAA
375016 TAGCAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 22 0.46
16 12 0.25
17 14 0.29
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:374991 original size:32 final size:31
Alignment explanation
Indices: 374945--375015 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 31
374935 CCTTTACACC
* **
374945 CAAAAACAAAAAAACAAAAAAGTAAAAAAAA
1 CAAAAAAAAAAAAACAAAAAACAAAAAAAAA
374976 CAAAAAAAAATAAAACAAAAAACAAAAAAAAA
1 CAAAAAAAAA-AAAACAAAAAACAAAAAAAAA
*
375008 GAAAAAAA
1 CAAAAAAA
375016 TAGCAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 9 0.26
32 26 0.74
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (31 bp):
CAAAAAAAAAAAAACAAAAAACAAAAAAAAA
Found at i:375025 original size:1 final size:1
Alignment explanation
Indices: 374946--375015 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
374936 CTTTACACCC
* * ** * * * * *
374946 AAAAACAAAAAAACAAAAAAGTAAAAAAAACAAAAAAAAATAAAACAAAAAACAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
375011 AAAAA
1 AAAAA
375016 TAGCAAAAAA
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:375028 original size:10 final size:10
Alignment explanation
Indices: 374960--375030 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
374950 ACAAAAAAAC
*
374960 AAAAAAGTA-
1 AAAAAAATAG
* *
374969 AAAAAAACAA
1 AAAAAAATAG
374979 AAAAAAATA-
1 AAAAAAATAG
* *
374988 AAACAAAAAAC
1 AAA-AAAATAG
*
374999 AAAAAAAAAG
1 AAAAAAATAG
375009 AAAAAAATAG
1 AAAAAAATAG
*
375019 CAAAAAATAG
1 AAAAAAATAG
375029 AA
1 AA
375031 GGGTCTAGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 10 0.20
10 38 0.75
11 3 0.06
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:376291 original size:29 final size:29
Alignment explanation
Indices: 376249--377789 Score: 2177
Period size: 28 Copynumber: 53.9 Consensus size: 29
376239 GTTCATCTCT
376249 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * * *
376278 TTTCAAAGCCCACAAATCAGTGGTACGCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376307 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376335 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376363 TTTCAAAGCCCACAACTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376391 TTTCAAAGCCCACAAGTCGGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376420 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
376449 TTTCAAAGCCCACAAATCAGTGGCACGCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376478 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376506 TTTCAAAGCCCGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376534 TTTCAAAGCCCACAACTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376562 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376591 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
376620 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376649 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376677 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376706 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376735 TTTCAAAGCCCACAAATCAGTGGCACT-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
376763 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376791 TTTCAAAGCCCACAACTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376819 TTTCAAAGCCCACAAGTCAGTGGCATTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376848 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
376877 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
376906 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
376934 TTTCAAAGCCCACAAGTTAGTGGCACTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
376963 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
376992 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377021 TTTTAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377049 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377077 TTTCAGAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
377105 TTTCGAAGGCCACAAGTCAGTGGCAC-CA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
377133 TTGCGAAGCCCACAATTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377161 TTTCAAAGCCCACAAGTCAGTGGCATTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377190 TTTCAAAGCCCACAAGTCAGTGGCATTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377219 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
377248 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377276 TTTCAAAGCCCACAAGTTAGTGGCACTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377305 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377334 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377362 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377391 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377420 TTTTAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377448 TTTCAAAGCCCACAAGTTAGTGGCACT-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377476 TTTTAGAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
377504 TTTCGAAGCCCACAAGTCAGTGGCAC-CA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
377532 TTGCGAAGCCCACAATTCAGTGGCACT-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
377560 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
377588 TTTTAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCC
* * * * *
377619 TTTTAAAGCTCACGCAAGTTAGTGGTAC-CT
1 TTTCAAAGC-C-CACAAGTCAGTGGCACTCC
377649 TTTCAAAGCCCACAAGTCAGTGGCACT-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
377677 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* * *
377705 TTTCAAAGCCCACGAGTTAGTGGCA-TTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
377733 TTTCAAAGCCCACGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCC
* *
377763 TTTTAAAGCCCATGCAAGTCAATGGCA
1 TTTCAAAGCCCA--CAAGTCAGTGGCA
377790 ACCCTTTTCA
Statistics
Matches: 1375, Mismatches: 115, Indels: 43
0.90 0.08 0.03
Matches are distributed among these distances:
27 1 0.00
28 671 0.49
29 616 0.45
30 62 0.05
31 25 0.02
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCC
Found at i:376508 original size:86 final size:86
Alignment explanation
Indices: 376249--377801 Score: 2197
Period size: 86 Copynumber: 18.1 Consensus size: 86
376239 GTTCATCTCT
* * *
376249 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGTACGCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
376314 GCCCACAAGTCAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* *
376335 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
376398 GCCCACAAGTCGGTGGCACTCC
66 GCCCACAAGTCAGTGGCAC-CC
* *
376420 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACGCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
376485 GCCCACAAGTCAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * *
376506 TTTCAAAGCCCGCAAGTCAGTGGCAC-CCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
376569 GCCCACAAGTCAGTGGCACTCC
66 GCCCACAAGTCAGTGGCAC-CC
* *
376591 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
376656 GCCCACAAGTTAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
*
376677 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
376742 GCCCACAAATCAGTGGCACTC
66 GCCCACAAGTCAGTGGCACCC
* *
376763 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
376826 GCCCACAAGTCAGTGGCATTCC
66 GCCCACAAGTCAGTGGCA-CCC
* * *
376848 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
376913 GCCCACAAGTTAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * *
376934 TTTCAAAGCCCACAAGTTAGTGGCACTTCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
376999 GCCCACAAATCAGTGGCACTCT
66 GCCCACAAGTCAGTGGCAC-CC
* * * *
377021 TTTTAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
377084 GCCCACAAGTCAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * * * * * *
377105 TTTCGAAGGCCACAAGTCAGTGGCAC-CATTGCGAAGCCCACAATTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
377168 GCCCACAAGTCAGTGGCATTCC
66 GCCCACAAGTCAGTGGCA-CCC
*
377190 TTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
377255 GCCCACAAGTCAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * *
377276 TTTCAAAGCCCACAAGTTAGTGGCACTTCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
377341 GCCCACAAGTTAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * * *
377362 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTTAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
377427 GCCCACAAGTCAGTGGCACCC
66 GCCCACAAGTCAGTGGCACCC
* * * * *
377448 TTTCAAAGCCCACAAGTTAGTGGCACT-CTTTTAGAGCCCACAAGTCAGTGGCAC-CCTTTCGAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
377511 GCCCACAAGTCAGTGGCACCA
66 GCCCACAAGTCAGTGGCACCC
* * * *
377532 TTGCGAAGCCCACAATTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
377595 GCCCACACAAGTCAGTGGCACTCC
66 G-CC-CACAAGTCAGTGGCAC-CC
* * * * *
377619 TTTTAAAGCTCACGCAAGTTAGTGGTAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCA
1 TTTCAAAGC-C-CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
377682 AAGCCCACAAGTCAGTGGCATCC
64 AAGCCCACAAGTCAGTGGCACCC
* * * *
377705 TTTCAAAGCCCACGAGTTAGTGGCA-TTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-A
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCA
*
377768 AAGCCCATGCAAGTCAATGGCAACCC
64 AAGCCCA--CAAGTCAGTGGC-ACCC
377794 TTTTCAAA
1 -TTTCAAA
377802 TCACCACTGT
Statistics
Matches: 1327, Mismatches: 111, Indels: 54
0.89 0.07 0.04
Matches are distributed among these distances:
84 253 0.19
85 242 0.18
86 609 0.46
87 153 0.12
88 17 0.01
89 46 0.03
90 7 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (86 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
GCCCACAAGTCAGTGGCACCC
Found at i:378343 original size:20 final size:19
Alignment explanation
Indices: 378315--378389 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
378305 TCATACCCTG
*
378315 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
378335 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
*
378355 ATGTATCGATATATTCTATA
1 ATGTATCGATACATT-TATA
378375 ATGTATCGATACATT
1 ATGTATCGATACATT
378390 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:378382 original size:40 final size:39
Alignment explanation
Indices: 378315--378392 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
378305 TCATACCCTG
*
378315 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCGATACAT-TATGA
* *
378355 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCGATACATTATG
378393 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCGATACATTATGA
Found at i:384226 original size:21 final size:20
Alignment explanation
Indices: 384188--384230 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
384178 TAAAAGCATA
* *
384188 AAAAAGAGAAGTAGAAAGGAT
1 AAAAAGAGAAGAACAAA-GAT
*
384209 AAAAAGAGGAGAACAAAGAT
1 AAAAAGAGAAGAACAAAGAT
384229 AA
1 AA
384231 GATTAAGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (20 bp):
AAAAAGAGAAGAACAAAGAT
Found at i:384945 original size:3 final size:3
Alignment explanation
Indices: 384937--384972 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
384927 CATACTTCTC
384937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
384973 TCTTAAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:386225 original size:42 final size:43
Alignment explanation
Indices: 386131--386233 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
386121 GATAGGAGTA
*
386131 TGTCCTGCTCTTCGAGGACAAAAGAAAAGAAGGAAATTAAATG
1 TGTCCTGCTCTTTGAGGACAAAAGAAAAGAAGGAAATTAAATG
* *
386174 TGTCATGCTCTTTGAGGACAAAAGAGAA-AAGGAAA-TAAA-G
1 TGTCCTGCTCTTTGAGGACAAAAGAAAAGAAGGAAATTAAATG
386214 TGCATCCTGCTCTTTGAGGA
1 TG--TCCTGCTCTTTGAGGA
386234 TAAAGGGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
40 3 0.06
41 4 0.07
42 22 0.41
43 25 0.46
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (43 bp):
TGTCCTGCTCTTTGAGGACAAAAGAAAAGAAGGAAATTAAATG
Found at i:386246 original size:42 final size:41
Alignment explanation
Indices: 386131--386246 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 41
386121 GATAGGAGTA
* *
386131 TGTCCTGCTCTTCGAGGACAAAAGAAAAGAAGGAAATTAAATG
1 TGTCCTGCTCTTTGAGGAC-AAAGGAAA-AAGGAAATTAAATG
* *
386174 TGTCATGCTCTTTGAGGACAAAAGAGAAAAGGAAA-TAAA-G
1 TGTCCTGCTCTTTGAGGACAAAGGA-AAAAGGAAATTAAATG
*
386214 TGCATCCTGCTCTTTGAGGATAAAGGGAAAAAG
1 TG--TCCTGCTCTTTGAGGACAAA-GGAAAAAG
386247 AAAGGAAGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 3 0.05
41 4 0.06
42 34 0.55
43 21 0.34
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (41 bp):
TGTCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATTAAATG
Found at i:386363 original size:61 final size:61
Alignment explanation
Indices: 386257--386943 Score: 856
Period size: 61 Copynumber: 11.3 Consensus size: 61
386247 AAAGGAAGCA
* * *
386257 CGTCCTGCTCTTT-AGGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTACAAGGAGAAA-A
1 CGTCCTGCTCTTTGA-GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGG
** * **
386318 CGTTTTGCTCTTTGAGGACTAAAAGGTGCCACCAGTTTGTGTGGGCTTTAAAAAGG-AAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGG
* * *
386379 CATCTTGCTTTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * *
386440 CATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTATATGGGCGTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
** *
386501 TATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAA-G
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * * *
386560 TGTCCTACTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * * * *
386621 AGTCTTGCTCTATGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAA--
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * *
386680 CATCCTGCTCTTTGAGAACTAGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* * *
386741 CGTCCTACTCTTTGGGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
*
386802 CGTCCTACTCTTTG-GAGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAG-GACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* ** * *
386863 CATTTTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* *
386924 CATCCTGCTCTTCGAGGACT
1 CGTCCTGCTCTTTGAGGACT
386944 GAAAGGATAA
Statistics
Matches: 550, Mismatches: 63, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
59 101 0.18
60 17 0.03
61 424 0.77
62 8 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (61 bp):
CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
Found at i:386649 original size:181 final size:180
Alignment explanation
Indices: 386258--386920 Score: 856
Period size: 181 Copynumber: 3.7 Consensus size: 180
386248 AAGGAAGCAC
* * *
386258 GTCCTGCTCTTT-AGGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTACAAGGAGAAA-ACGT
1 GTCCTGCTCTTTGA-GGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGA-AAAGGCAT
** * ** * * *
386321 TTTGCTCTTTGAGGACTAAAAGGTGCCACCAGTTTGTGTGGGCTTTAAAAAGGAAAGGCATCTTG
64 CCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTAGGCTTT-AAAAGGAAAGG--TCCTA
* *
386386 CTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
126 CTATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG-A
* * *
386442 -TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTATATGGGCGTTAAAAGGAAAAGGTATC
1 GTCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATC
* *
386505 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTGTCCTACTA
65 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAG-GTCCTACTA
*
386570 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGA
129 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGA
* * *
386622 GTCTTGCTCTATGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAA--CATCC
1 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCC
*
386685 TGCTCTTTGAGAACTAGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACT
66 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGG-AAA-G-GTCCTACT
* * * * *
386750 CTTTGGGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGC
128 ATTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGA
* * *
386803 GTCCTACTCTTTG-GAGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATT
1 GTCCTGCTCTTTGAG-GACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATC
* *
386867 TTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAA
65 CTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAA
386921 AGGCATCCTG
Statistics
Matches: 425, Mismatches: 42, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
179 51 0.12
180 5 0.01
181 211 0.50
182 18 0.04
183 139 0.33
184 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (180 bp):
GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCC
TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAGGTCCTACTATT
TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGA
Found at i:387909 original size:7 final size:7
Alignment explanation
Indices: 387894--387946 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
387884 AAGTAGGTTC
387894 TTTTCTT
1 TTTTCTT
*
387901 TTCTCTT
1 TTTTCTT
387908 TTTTCTT
1 TTTTCTT
387915 TTTTCTT
1 TTTTCTT
387922 TTTTCATT
1 TTTTC-TT
387930 TTTT-TT
1 TTTTCTT
387936 GTTGTTCTT
1 -TT-TTCTT
387945 TT
1 TT
387947 GTTTCATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 2 0.05
7 26 0.65
8 10 0.25
9 2 0.05
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:397670 original size:19 final size:18
Alignment explanation
Indices: 397646--397740 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
397636 ATCCATACAA
397646 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
397665 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
397678 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
397697 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
397710 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
397729 TGTATCGATACA
1 TGTATCGATACA
397741 ATGTATCGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 34 0.53
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:397676 original size:32 final size:32
Alignment explanation
Indices: 397632--397748 Score: 216
Period size: 32 Copynumber: 3.7 Consensus size: 32
397622 TTTCAACGAT
*
397632 TTGTATCCATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
397664 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
397696 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
397728 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
397749 CTACGAAGCT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:397683 original size:13 final size:13
Alignment explanation
Indices: 397665--397721 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
397655 ACATAAGTGT
397665 TGTATCGATACAA
1 TGTATCGATACAA
397678 TGTATCGATACATAA
1 TGTATCGATAC--AA
397693 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
397710 TGTATCGATACA
1 TGTATCGATACA
397722 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:397811 original size:13 final size:13
Alignment explanation
Indices: 397793--397817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
397783 ATTACTCAAA
397793 TGTATCGATACAT
1 TGTATCGATACAT
397806 TGTATCGATACA
1 TGTATCGATACA
397818 CTGATCTTTG
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:397870 original size:52 final size:52
Alignment explanation
Indices: 397826--397954 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 52
397816 CACTGATCTT
* *
397826 TGTATCGATACATGCAGGTAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * * *
397878 TGTATCAATATATACAGGCAAATTTGCCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
397930 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
397955 TCATATTTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:404214 original size:51 final size:51
Alignment explanation
Indices: 404158--404256 Score: 173
Period size: 51 Copynumber: 1.9 Consensus size: 51
404148 GAAATATCCC
404158 CGATTGTGAAAAATTAGTGTTTTGGAAATAAAA-CCGGGGTTAGAGTATTTT
1 CGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCC-GGGTTAGAGTATTTT
*
404209 CGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCCGGGTTAGAGTAT
1 CGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCCGGGTTAGAGTAT
404257 CCCCTCGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.34
Consensus pattern (51 bp):
CGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCCGGGTTAGAGTATTTT
Found at i:404284 original size:79 final size:79
Alignment explanation
Indices: 404192--404495 Score: 380
Period size: 79 Copynumber: 3.8 Consensus size: 79
404182 GAAATAAAAC
* * * * *
404192 CGGGGTTAGAGTATTTTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCC-GGGTTAGAGTA
1 CGGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAA-CCAGGGTTGGAGTA
404256 TCCCCTCGAAAATAA
65 TCCCCTCGAAAATAA
* * *
404271 CGGGGTTGGAGTATC-CTTGATTGTGAAAAATTAGTGTTTTGAAAATAAAACCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCTC-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTA
***
404335 TCATTTCGAAAATAA
65 TCCCCTCGAAAATAA
* * * *
404350 CGCGGTTGGAGTATCTCCGATTGTAAAAAATTGGTATTTTGGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTAT
* *
404415 CCCCTCGGAATTAA
66 CCCCTCGAAAATAA
* * *
404429 CAGGGTTGGAGTATGC-CCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTA
1 CGGGGTTGGAGTAT-CTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTA
404493 TCC
65 TCC
404496 ACGATTGTGA
Statistics
Matches: 192, Mismatches: 29, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
78 2 0.01
79 188 0.98
80 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (79 bp):
CGGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTAT
CCCCTCGAAAATAA
Found at i:404488 original size:158 final size:158
Alignment explanation
Indices: 404195--404494 Score: 460
Period size: 158 Copynumber: 1.9 Consensus size: 158
404185 ATAAAACCGG
* * * *
404195 GGTTAGAGTATTTTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCCGGGTTAGAGTATCCC
1 GGTTAGAGTATCTCCGATTGTAAAAAATTGGTATTTTGGAAATAAAATCCGGGTTAGAGTATCCC
* *
404260 CTCGAAAATAACGGGGTTGGAGTATCCTTGATTGTGAAAAATTAGTGTTTTGAAAATAAAACCGG
66 CTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGAAAATAAAACCGG
404325 GGTTGGAGTATCATTTCGAAAATAACGC
131 GGTTGGAGTATCATTTCGAAAATAACGC
* *
404353 GGTTGGAGTATCTCCGATTGTAAAAAATTGGTATTTTGGAAATAAAA-CCAGGGTTGGAGTATCC
1 GGTTAGAGTATCTCCGATTGTAAAAAATTGGTATTTTGGAAATAAAATCC-GGGTTAGAGTATCC
* * * *
404417 CCTCGGAATTAACAGGGTTGGAGTATGCC-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAATC
65 CCTCGAAAATAACAGGGTTGGAGTAT-CCTCGATTGTGAAAAATTAGTGTTTTGAAAATAAAACC
404481 GGGGTTGGAGTATC
129 GGGGTTGGAGTATC
404495 CACGATTGTG
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
157 2 0.02
158 124 0.97
159 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (158 bp):
GGTTAGAGTATCTCCGATTGTAAAAAATTGGTATTTTGGAAATAAAATCCGGGTTAGAGTATCCC
CTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGAAAATAAAACCGG
GGTTGGAGTATCATTTCGAAAATAACGC
Found at i:404507 original size:51 final size:50
Alignment explanation
Indices: 404431--404547 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 50
404421 GGAATTAACA
*
404431 GGGTTGGAGTATGCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCG
1 GGGTTGGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
404482 GGGTTGGAGTATCCACGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCG
1 GGGTTGGAGTATCC-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
* *
404533 AGATTGGAGTATCCC
1 GGGTTGGAGTATCCC
404548 CTCGAAAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 3 0.05
51 58 0.95
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
Found at i:406972 original size:20 final size:20
Alignment explanation
Indices: 406947--407049 Score: 107
Period size: 20 Copynumber: 4.8 Consensus size: 20
406937 TAAAACCCAG
406947 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
406967 AATGTATCGATATAATGAAC
1 AATGTATCGATACAATGAAC
*
406987 AATGTATCGATACATCTGGTAAACCC
1 AATGTATCGATACA-AT-G--AA--C
407013 AAAATGTATCGATACAATGAAC
1 --AATGTATCGATACAATGAAC
*
407035 AATGTATCAATACAA
1 AATGTATCGATACAA
407050 ATTGTGAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
20 46 0.66
21 1 0.01
22 2 0.03
24 4 0.06
26 2 0.03
27 1 0.01
28 14 0.20
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:407033 original size:68 final size:70
Alignment explanation
Indices: 406897--407049 Score: 238
Period size: 68 Copynumber: 2.2 Consensus size: 70
406887 AAAATGCCTG
* *
406897 AATGTATCAATACATTGAAAAATGTATCAATACATCTGGGTAAAACCCAGAATGTATCGATACAA
1 AATGTATCAATACAATGAAAAATGTATCAATACATCTGGGTAAAACCCAAAATGTATCGATACAA
406962 TGAAC
66 TGAAC
* * * *
406967 AATGTATCGATATAATGAACAATGTATCGATACATCT-GGT-AAACCCAAAATGTATCGATACAA
1 AATGTATCAATACAATGAAAAATGTATCAATACATCTGGGTAAAACCCAAAATGTATCGATACAA
407030 TGAAC
66 TGAAC
407035 AATGTATCAATACAA
1 AATGTATCAATACAA
407050 ATTGTGAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
68 40 0.53
69 3 0.04
70 32 0.43
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (70 bp):
AATGTATCAATACAATGAAAAATGTATCAATACATCTGGGTAAAACCCAAAATGTATCGATACAA
TGAAC
Found at i:411173 original size:20 final size:20
Alignment explanation
Indices: 411150--411222 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
411140 ACAATTCAAA
411150 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
411170 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
411191 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
411211 GTATCGATACAT
1 GTATCGATACAT
411223 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:411194 original size:21 final size:21
Alignment explanation
Indices: 411168--411243 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
411158 ACATGTTGCA
411168 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
411189 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
411209 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
411230 ATGTATCGATACAT
1 ATGTATCGATACAT
411244 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:411201 original size:41 final size:41
Alignment explanation
Indices: 411150--411243 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
411140 ACAATTCAAA
*
411150 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
411191 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
411232 GTATCGATACAT
1 GTATCGATACAT
411244 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:411300 original size:13 final size:13
Alignment explanation
Indices: 411282--411307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
411272 TACAGCAAGT
411282 ATGTATCGATACA
1 ATGTATCGATACA
411295 ATGTATCGATACA
1 ATGTATCGATACA
411308 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:413554 original size:21 final size:21
Alignment explanation
Indices: 413521--413565 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
413511 TTGCAAGTTG
*
413521 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
413543 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
413563 AAA
1 AAA
413566 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:417496 original size:13 final size:13
Alignment explanation
Indices: 417478--417515 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
417468 CATTTTTATT
417478 TGTATCGATACAA
1 TGTATCGATACAA
*
417491 TGTATCGATACAC
1 TGTATCGATACAA
417504 TGTATCGATACA
1 TGTATCGATACA
417516 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:419967 original size:20 final size:20
Alignment explanation
Indices: 419944--420016 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
419934 ACAATTCAAA
419944 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
419964 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
419985 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
420005 GTATCGATACAT
1 GTATCGATACAT
420017 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:419988 original size:21 final size:21
Alignment explanation
Indices: 419962--420037 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
419952 ACATGTTGCA
419962 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
419983 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
420003 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
420024 ATGTATCGATACAT
1 ATGTATCGATACAT
420038 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:419995 original size:41 final size:41
Alignment explanation
Indices: 419944--420037 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
419934 ACAATTCAAA
*
419944 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
419985 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
420026 GTATCGATACAT
1 GTATCGATACAT
420038 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:420094 original size:13 final size:13
Alignment explanation
Indices: 420076--420101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420066 TACAGCAAGT
420076 ATGTATCGATACA
1 ATGTATCGATACA
420089 ATGTATCGATACA
1 ATGTATCGATACA
420102 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:421390 original size:13 final size:13
Alignment explanation
Indices: 421372--421396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
421362 CAATTTTTTG
421372 TGTATCGATACAT
1 TGTATCGATACAT
421385 TGTATCGATACA
1 TGTATCGATACA
421397 AGTTTGGCTA
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:422403 original size:13 final size:13
Alignment explanation
Indices: 422385--422409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422375 CATAAAATGT
422385 TGTATCGATACAA
1 TGTATCGATACAA
422398 TGTATCGATACA
1 TGTATCGATACA
422410 TATTTTTTGT
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:422425 original size:32 final size:33
Alignment explanation
Indices: 422365--422430 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
422355 TTCAACGATT
422365 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
422398 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
422430 T
1 T
422431 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:422489 original size:13 final size:13
Alignment explanation
Indices: 422471--422495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422461 ATTACTCAAA
422471 TGTATCGATACAT
1 TGTATCGATACAT
422484 TGTATCGATACA
1 TGTATCGATACA
422496 CTGATCTTTG
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:422597 original size:52 final size:52
Alignment explanation
Indices: 422504--422631 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
422494 CACTGATCTT
*
422504 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
422555 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
422607 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
422632 TCATATTTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.26
52 54 0.74
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:425800 original size:20 final size:21
Alignment explanation
Indices: 425762--425800 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
425752 GTAATTTACA
*
425762 CACATATCAAAAATTTATTTG
1 CACATATCAAAAATCTATTTG
*
425783 CACATA-CAAACATCTATT
1 CACATATCAAAAATCTATT
425801 CTCTCCCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
CACATATCAAAAATCTATTTG
Found at i:427583 original size:13 final size:13
Alignment explanation
Indices: 427565--427636 Score: 84
Period size: 13 Copynumber: 6.0 Consensus size: 13
427555 ATAATCCCCC
*
427565 TGTATCGATACAG
1 TGTATCGATACAA
427578 TGTATCGATACAA
1 TGTATCGATACAA
427591 TGTATCGATACAA
1 TGTATCGATACAA
*
427604 ---A--GA-AAAA
1 TGTATCGATACAA
427611 TGTATCGATACAA
1 TGTATCGATACAA
427624 TGTATCGATACAA
1 TGTATCGATACAA
427637 AGAAAAATGT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
10 2 0.04
12 2 0.04
13 41 0.82
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:427614 original size:20 final size:20
Alignment explanation
Indices: 427589--427655 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
427579 GTATCGATAC
427589 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
427609 AATGTATCGATAC-------
1 AATGTATCGATACAAAGAAA
427622 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
427642 AATGTATCGATACA
1 AATGTATCGATACA
427656 TTGAATTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:427620 original size:33 final size:33
Alignment explanation
Indices: 427578--427655 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
427568 ATCGATACAG
427578 TGTATCGATACAATGTATCGATACAAAGAAAAA
1 TGTATCGATACAATGTATCGATACAAAGAAAAA
427611 TGTATCGATACAATGTATCGATACAAAGAAAAA
1 TGTATCGATACAATGTATCGATACAAAGAAAAA
427644 TGTATCGATACA
1 TGTATCGATACA
427656 TTGAATTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAAAGAAAAA
Found at i:429727 original size:15 final size:15
Alignment explanation
Indices: 429707--429737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
429697 ATTTCGTTAC
*
429707 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
429722 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
429737 G
1 G
429738 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:433831 original size:13 final size:13
Alignment explanation
Indices: 433813--433838 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
433803 CAATTTTTTG
433813 TGTATCGATACAT
1 TGTATCGATACAT
433826 TGTATCGATACAT
1 TGTATCGATACAT
433839 ACTTTGTGTA
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:433850 original size:32 final size:33
Alignment explanation
Indices: 433793--433856 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
433783 TACAAGCCAA
**
433793 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
433826 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
433857 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:436814 original size:31 final size:31
Alignment explanation
Indices: 436779--436848 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
436769 ACAAGGTTAA
436779 AATTAGCAAATTGCTTGCTAGATTCCTAGTT
1 AATTAGCAAATTGCTTGCTAGATTCCTAGTT
436810 AATTAGCAAATTGCTTGCTAGATTCCTAGTT
1 AATTAGCAAATTGCTTGCTAGATTCCTAGTT
436841 AATTAGCA
1 AATTAGCA
436849 CATCACTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (31 bp):
AATTAGCAAATTGCTTGCTAGATTCCTAGTT
Found at i:438202 original size:20 final size:19
Alignment explanation
Indices: 438177--438241 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
438167 AGATGTATCA
438177 ATACATTTTTCAATGCATCG
1 ATACATTTTT-AATGCATCG
* * * *
438197 ATACATGTATGAATGTATTG
1 ATACAT-TTTTAATGCATCG
438217 AT--ATTGTTTAATGCATCG
1 ATACATT-TTTAATGCATCG
438235 ATACATT
1 ATACATT
438242 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.36
20 18 0.55
21 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (19 bp):
ATACATTTTTAATGCATCG
Found at i:440687 original size:97 final size:97
Alignment explanation
Indices: 440535--440715 Score: 229
Period size: 97 Copynumber: 1.9 Consensus size: 97
440525 ATTGTCAAGA
* * ** * ** **
440535 TTTAAATCTTATTCTTGCCTAAATTGTCATCATTGGGGACATTTTAACCCTATTCCTCTTAGGAA
1 TTTAAATCTTATTCTCGCCTAAATTGCCATCACCGGGGACACTCCAACCCTATTCCTCCGAGGAA
440600 ATACTCCAACCCCGCTTTTAAACTCATCAAAG
66 ATACTCCAACCCCGCTTTTAAACTCATCAAAG
* *
440632 TTTAAATCTTATTCTCGCTTAAATTGCCATCACCGGGGACACTCCAATCCC-ATTCCTCCGAGGG
1 TTTAAATCTTATTCTCGCCTAAATTGCCATCACCGGGGACACTCCAA-CCCTATTCCTCCGAGGA
* *
440696 GATACTCCAACCCCGTTTTT
65 AATACTCCAACCCCGCTTTT
440716 TAATAAAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
97 67 0.96
98 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (97 bp):
TTTAAATCTTATTCTCGCCTAAATTGCCATCACCGGGGACACTCCAACCCTATTCCTCCGAGGAA
ATACTCCAACCCCGCTTTTAAACTCATCAAAG
Found at i:450412 original size:13 final size:13
Alignment explanation
Indices: 450394--450418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450384 CATAAAATGT
450394 TGTATCGATACAA
1 TGTATCGATACAA
450407 TGTATCGATACA
1 TGTATCGATACA
450419 TATTTTTTTG
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:450416 original size:33 final size:33
Alignment explanation
Indices: 450374--450443 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
450364 TTCAACGATT
450374 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
450407 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
450440 TGTA
1 TGTA
450444 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:450500 original size:13 final size:13
Alignment explanation
Indices: 450482--450506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450472 ATTACTCACA
450482 TGTATCGATACAT
1 TGTATCGATACAT
450495 TGTATCGATACA
1 TGTATCGATACA
450507 CTGATCTTTG
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:460089 original size:19 final size:19
Alignment explanation
Indices: 460065--460129 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 19
460055 TAGCCAAACT
460065 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
*
460084 TGTATC-A-ATAC---A-A
1 TGTATCGATACACAAAATA
460097 TGTATCGATACACATAAAATA
1 TGTATCGATACAC--AAAATA
460118 TGTATCGATACA
1 TGTATCGATACA
460130 TTGGCTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 7 0.19
14 2 0.06
15 3 0.08
17 3 0.08
18 1 0.03
19 6 0.17
20 1 0.03
21 13 0.36
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:460106 original size:32 final size:33
Alignment explanation
Indices: 460065--460129 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
460055 TAGCCAAACT
460065 TGTATCGATACAC-AAAATATGTATCAATACAA
1 TGTATCGATACACAAAAATATGTATCAATACAA
*
460097 TGTATCGATACACATAAAATATGTATCGATACA
1 TGTATCGATACACA-AAAATATGTATCAATACA
460130 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
34 17 0.57
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCAATACAA
Found at i:462362 original size:21 final size:21
Alignment explanation
Indices: 462329--462378 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
462319 TTGCAAGTTG
*
462329 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
462351 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
462372 AAATAAA
1 AAATAAA
462379 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:464196 original size:15 final size:15
Alignment explanation
Indices: 464176--464206 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
464166 TAAAAATGTC
*
464176 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
464191 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
464206 C
1 C
464207 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:466305 original size:13 final size:13
Alignment explanation
Indices: 466287--466324 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
466277 CATTTTTCTT
466287 TGTATCGATACAA
1 TGTATCGATACAA
*
466300 TGTATCGATACAC
1 TGTATCGATACAA
466313 TGTATCGATACA
1 TGTATCGATACA
466325 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:468908 original size:32 final size:33
Alignment explanation
Indices: 468865--468929 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
468855 TAGCCAAACT
468865 TGTATCAATACAC-AAAATATGTATCAATACAA
1 TGTATCAATACACAAAAATATGTATCAATACAA
* *
468897 TGTATCGATACACATAAAATATGTATCGATACA
1 TGTATCAATACACA-AAAATATGTATCAATACA
468930 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
34 17 0.59
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (33 bp):
TGTATCAATACACAAAAATATGTATCAATACAA
Found at i:472004 original size:20 final size:21
Alignment explanation
Indices: 471969--472007 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
471959 AAAAATAATT
471969 ATATATAAATAAATTAATAAA
1 ATATATAAATAAATTAATAAA
*
471990 ATATATTAA-AAATTAATA
1 ATATATAAATAAATTAATA
472008 TAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATATAAATAAATTAATAAA
Found at i:472374 original size:2 final size:2
Alignment explanation
Indices: 472367--472398 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
472357 ACATCGCACG
*
472367 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
472399 ACAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:474020 original size:6 final size:6
Alignment explanation
Indices: 474009--474036 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
473999 AAATATTTTT
474009 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
474037 TATATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:474486 original size:7 final size:7
Alignment explanation
Indices: 474471--474500 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
474461 ATGGTGGTTC
*
474471 ATTTCTT
1 ATTTGTT
474478 ATTTGTT
1 ATTTGTT
474485 ATTTGTT
1 ATTTGTT
474492 ATTTGTT
1 ATTTGTT
474499 AT
1 AT
474501 GTGGTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.10, T:0.70
Consensus pattern (7 bp):
ATTTGTT
Found at i:475121 original size:25 final size:27
Alignment explanation
Indices: 475093--475148 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
475083 TTTAAAATTT
*
475093 ATATAATATAAA-TTAT-TAATTAT-TA
1 ATATAATA-AAATTTATATAAATATATA
*
475118 ATATATTAAAATTTATATAAATATATA
1 ATATAATAAAATTTATATAAATATATA
475145 ATAT
1 ATAT
475149 TTTAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 11 0.42
26 6 0.23
27 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATAATAAAATTTATATAAATATATA
Found at i:475377 original size:27 final size:27
Alignment explanation
Indices: 475338--475421 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 27
475328 GTTTGATTTA
*
475338 TTTAAATTAAAAATTAATTTAATTAAT
1 TTTAAATTAAAAATTAAATTAATTAAT
475365 TTTAATATTAAAATTGATTAAATTAATTAAT
1 TTTAA-ATTAAAA---ATTAAATTAATTAAT
* *
475396 TTTAAATTTAAAATTAAAATAATTAA
1 TTTAAATTAAAAATTAAATTAATTAA
475422 ATTAATATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 18 0.36
28 7 0.14
30 6 0.12
31 19 0.38
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TTTAAATTAAAAATTAAATTAATTAAT
Found at i:475389 original size:36 final size:36
Alignment explanation
Indices: 475348--475432 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 36
475338 TTTAAATTAA
* * *
475348 AAATTAATTTAA-TTAATTTTAATATTAAAATTGATT
1 AAATTAATTTAATTTAAATTTAAAATTAAAA-TAATT
475384 AAATTAA-TTAATTTTAAATTTAAAATTAAAATAATT
1 AAATTAATTTAA-TTTAAATTTAAAATTAAAATAATT
475420 AAATTAATATTAA
1 AAATTAAT-TTAA
475433 AGTTGATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 4 0.10
36 18 0.43
37 16 0.38
38 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
AAATTAATTTAATTTAAATTTAAAATTAAAATAATT
Found at i:475391 original size:31 final size:31
Alignment explanation
Indices: 475350--475441 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
475340 TAAATTAAAA
*
475350 ATTAATTTAATTAATTTTAATATTAAAATTG
1 ATTAAATTAATTAATTTTAATATTAAAATTG
475381 ATTAAATTAATTAATTTTAA-ATTTAAAATT-
1 ATTAAATTAATTAATTTTAATA-TTAAAATTG
* *
475411 A--AAA-TAATTAA-ATTAATATTAAAGTTG
1 ATTAAATTAATTAATTTTAATATTAAAATTG
475438 ATTA
1 ATTA
475442 GTTTGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
26 11 0.21
27 9 0.17
28 3 0.06
29 1 0.02
30 2 0.04
31 27 0.51
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTAAATTAATTAATTTTAATATTAAAATTG
Found at i:475400 original size:15 final size:15
Alignment explanation
Indices: 475351--475403 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
475341 AAATTAAAAA
*
475351 TTAATTTAATTAATT
1 TTAAATTAATTAATT
475366 TTAATATTAA--AATT
1 TTAA-ATTAATTAATT
475380 GATTAAATTAATTAATT
1 --TTAAATTAATTAATT
475397 TTAAATT
1 TTAAATT
475404 TAAAATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 4 0.12
15 16 0.50
16 8 0.25
17 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTAAATTAATTAATT
Found at i:475475 original size:20 final size:21
Alignment explanation
Indices: 475443--475543 Score: 79
Period size: 20 Copynumber: 4.9 Consensus size: 21
475433 AGTTGATTAG
475443 TTTG-ATT-TTTTTAATTTT-
1 TTTGAATTATTTTTAATTTTA
475461 TTTGAATTATTTTT-ATTTT-
1 TTTGAATTATTTTTAATTTTA
*
475480 TTTGATTATTTTTTTTAATTTTA
1 TTTGA--ATTATTTTTAATTTTA
* * *
475503 ATTGAATT-TTATTATTTTTA
1 TTTGAATTATTTTTAATTTTA
*
475523 TTTTAATTAGGTTTTTAATTT
1 TTTGAATTA--TTTTTAATTT
475544 AAGTTTAGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.06
19 13 0.20
20 21 0.32
21 11 0.17
22 5 0.08
23 12 0.18
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (21 bp):
TTTGAATTATTTTTAATTTTA
Found at i:475478 original size:19 final size:19
Alignment explanation
Indices: 475443--475492 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
475433 AGTTGATTAG
475443 TTTGATT-TTTTTAATTTT
1 TTTGATTATTTTTAATTTT
475461 TTTGAATTATTTTT-ATTTT
1 TTTG-ATTATTTTTAATTTT
475480 TTTGATTATTTTT
1 TTTGATTATTTTT
475493 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.43
19 12 0.40
20 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTGATTATTTTTAATTTT
Done.