Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 170 of 325
Found at i:55093808 original size:129 final size:130
Alignment explanation
Indices: 55093551--55093798 Score: 330
Period size: 133 Copynumber: 1.9 Consensus size: 130
55093541 ATTAATCAGC
*
55093551 CAATTATGATAACTAGTGAGCATGGATTGATGAATGTTCCATTAGGTTTTATATATGTATCTAAT
1 CAATTATGATAACTAGTGAGCATGGATTGATGAATGTTCCATTAGGTTTTATATATATATCTAAT
* * *
55093616 GTGTATGTATTATGTGTACTACTATGCTTCACTAGGAGTAAAGGCAAATCTGGTGTGAAACTAAG
66 GTATATCTATTATGTGTACTAC-ATGCTTCACTAGGAATAAAGGCAAATCTGGTGTGAAACTAAG
55093681 T
130 T
* *
55093682 CAATTATGATGACTAGTGAGCATGGATATTGATGAATGTTCCATTAGTTTTTATATATAATATCT
1 CAATTATGATAACTAGTGAGCATGG--ATTGATGAATGTTCCATTAGGTTTTATATAT-ATATCT
55093747 ATATGTAT-TCTATATAT-T-T-CT-C-TGCTTCACT-GGCAATAAAGGCAAATCTGGT
63 A-ATGTATATCTAT-TATGTGTACTACATGCTTCACTAGG-AATAAAGGCAAATCTGGT
55093799 ATTGAACTAA
Statistics
Matches: 105, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
128 2 0.02
129 26 0.25
131 25 0.24
132 2 0.02
133 31 0.30
134 11 0.10
135 8 0.08
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (130 bp):
CAATTATGATAACTAGTGAGCATGGATTGATGAATGTTCCATTAGGTTTTATATATATATCTAAT
GTATATCTATTATGTGTACTACATGCTTCACTAGGAATAAAGGCAAATCTGGTGTGAAACTAAGT
Found at i:55094542 original size:18 final size:20
Alignment explanation
Indices: 55094507--55094547 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
55094497 ATATAATTTT
*
55094507 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
55094527 AAAATAT-TA-AAAACATCA
1 AAAATATATATAAAACATCA
55094545 AAA
1 AAA
55094548 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:55096454 original size:33 final size:32
Alignment explanation
Indices: 55096383--55096468 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
55096373 AGATTATGAG
* *
55096383 AATTTTCAAAAAATTTTAAGAA-AGTTTAATTAA
1 AATTTTC-AAAAACTTTAA-AAGAGTATAATTAA
*
55096416 AATTTTCAAAAA-TTTAAAAGAGTATATTTAA
1 AATTTTCAAAAACTTTAAAAGAGTATAATTAA
*
55096447 AATATTTTAAAAACTTTAAAAG
1 AAT-TTTCAAAAACTTTAAAAG
55096469 TATAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.04
31 17 0.36
32 13 0.28
33 15 0.32
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (32 bp):
AATTTTCAAAAACTTTAAAAGAGTATAATTAA
Found at i:55096510 original size:9 final size:9
Alignment explanation
Indices: 55096496--55096538 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
55096486 AATTAAATTT
55096496 TTTTAAAAA
1 TTTTAAAAA
55096505 TTTTAAAAAA
1 TTTT-AAAAA
*
55096515 ATTT-AAAA
1 TTTTAAAAA
*
55096523 TTTTTAAAA
1 TTTTAAAAA
55096532 TTTTAAA
1 TTTTAAA
55096539 GCGCAAACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:55100599 original size:43 final size:43
Alignment explanation
Indices: 55100519--55100600 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
55100509 AATATAAGTG
* ** *
55100519 GCATCCGAGCTCGTTAAGAGGTTCGAGTTTGTTATGGATGCCA
1 GCATCCGAGCTCGTTAAGAGGTCCGAGTTCATGATGGATGCCA
* *
55100562 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATGATGGAT
1 GCATCCGAGCTCGTTAAGAGGTCCGAGTTCATGATGGAT
55100601 ACGATACATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (43 bp):
GCATCCGAGCTCGTTAAGAGGTCCGAGTTCATGATGGATGCCA
Found at i:55106971 original size:46 final size:48
Alignment explanation
Indices: 55106864--55106977 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
55106854 TGTCTTCGAC
** * * *
55106864 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATCTAAT
* *
55106912 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCAT-T-TATCTGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATCTAAT
55106958 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
55106978 TCTGTCCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 26 0.45
47 1 0.02
48 31 0.53
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATCTAAT
Found at i:55113198 original size:5 final size:5
Alignment explanation
Indices: 55113188--55113215 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55113178 ATAATTTGAT
55113188 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
55113216 GGAAAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:55114138 original size:25 final size:25
Alignment explanation
Indices: 55114100--55114165 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
55114090 GATTCTCAGG
*
55114100 TCGAGAGAGCTTACTGATATTTAGC
1 TCGAGAGAGCTTACCGATATTTAGC
** *
55114125 TCGAGAGATTTTACCGGTATTTAGC
1 TCGAGAGAGCTTACCGATATTTAGC
*
55114150 TCGCA-TGAGCTTACCG
1 TCG-AGAGAGCTTACCG
55114166 TTACTCAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (25 bp):
TCGAGAGAGCTTACCGATATTTAGC
Found at i:55115918 original size:24 final size:24
Alignment explanation
Indices: 55115890--55115950 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
55115880 AACCGTATTT
* * *
55115890 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
55115914 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
55115938 GCACACATAGTGC
1 GCACACATAGTGC
55115951 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:55120285 original size:49 final size:49
Alignment explanation
Indices: 55120064--55120567 Score: 802
Period size: 47 Copynumber: 10.6 Consensus size: 49
55120054 CCCTTCGGGA
* * * * *
55120064 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55120111 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55120158 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120205 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120252 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55120301 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120350 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120397 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120444 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55120493 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120542 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
55120568 CACAATTATC
Statistics
Matches: 433, Mismatches: 18, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 232 0.54
49 200 0.46
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55120400 original size:192 final size:192
Alignment explanation
Indices: 55120064--55120567 Score: 863
Period size: 192 Copynumber: 2.6 Consensus size: 192
55120054 CCCTTCGGGA
* * * * * * *
55120064 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
* *
55120125 ACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
*
55120190 CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120252 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
55120317 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
55120382 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55120444 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
* *
55120509 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATACATTCACAT
66 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACAT
55120568 CACAATTATC
Statistics
Matches: 298, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
188 10 0.03
189 1 0.00
190 37 0.12
192 250 0.84
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (192 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55123872 original size:48 final size:48
Alignment explanation
Indices: 55123797--55124018 Score: 208
Period size: 48 Copynumber: 4.7 Consensus size: 48
55123787 CACATGGTAG
* * * * *
55123797 GATGTCAATGCCATATCCCGGATATGGTCTTACATTGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
*** **
55123845 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTGTAGGTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
55123893 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * ** * *
55123941 GATG-C--TG--ATAG-CCCAG-CTATGGTCTTATACGAAATTACATATA
1 GATGCCAATGCCAT-GTCCCAGAC-ATGGTCTTACATGGGATCACATATC
*
55123984 GATGCCAAAT-CCATGTCACAGACATGGTCTTACAT
1 GATGCC-AATGCCATGTCCCAGACATGGTCTTACAT
55124019 AAGATTGTAC
Statistics
Matches: 140, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.21
44 2 0.01
45 2 0.01
47 3 0.02
48 101 0.72
49 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:55130210 original size:48 final size:47
Alignment explanation
Indices: 55130158--55130272 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 47
55130148 TATCCTGAAT
*
55130158 ATGGTATTACTTGGGATCACGTA-TCAATGCCAATGCCATGTCCCAGGC
1 ATGGTATTACATGGGAT--CGTAGTCAATGCCAATGCCATGTCCCAGGC
* * **
55130206 ATGGTCTTACATGGGATCGTAGGTCGATGCCAATGCCATGTCCCAAAC
1 ATGGTATTACATGGGATCGTA-GTCAATGCCAATGCCATGTCCCAGGC
* *
55130254 ATAGTCTTACATGGGATCG
1 ATGGTATTACATGGGATCG
55130273 CATATCGGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
46 4 0.07
48 55 0.93
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (47 bp):
ATGGTATTACATGGGATCGTAGTCAATGCCAATGCCATGTCCCAGGC
Found at i:55134136 original size:41 final size:41
Alignment explanation
Indices: 55134089--55134183 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
55134079 ACGGCTTGGC
*
55134089 ACACGCCCGTGTCCCTGGCCAGTGCCCTTCACACTGCCATG
1 ACACGCCCGTGTCCCTGGCCAGTGCCCTTCACACGGCCATG
*
55134130 ACACGCCCGTGTCCCTGGCCAGTGTCCTTCACACGGCCATG
1 ACACGCCCGTGTCCCTGGCCAGTGCCCTTCACACGGCCATG
55134171 ACACGCCCGTGTC
1 ACACGCCCGTGTC
55134184 TTAGCCCTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.15, C:0.43, G:0.23, T:0.19
Consensus pattern (41 bp):
ACACGCCCGTGTCCCTGGCCAGTGCCCTTCACACGGCCATG
Found at i:55135223 original size:44 final size:46
Alignment explanation
Indices: 55135165--55135321 Score: 144
Period size: 46 Copynumber: 3.4 Consensus size: 46
55135155 CATGTTCCGA
*
55135165 ACATGGTCTTACACTAGCTTA-A-CTTGTA-GCCGATGCATGTCCCAG
1 ACAT-GTCTTACACTAGCTTACATCTCG-AGGCCGATGCATGTCCCAG
* * *
55135210 ACATGTCTTACACTGGCTTACATCTCGAGGCTGATGCATGTCCTAG
1 ACATGTCTTACACTAGCTTACATCTCGAGGCCGATGCATGTCCCAG
* * * * *
55135256 ACGTGTCTTACACTAGCTCT-CATCTC-ACTGCTGATGCCATGTTCCGG
1 ACATGTCTTACACTAGCT-TACATCTCGA-GGCCGATG-CATGTCCCAG
55135303 ACATGGTCTTACACTAGCT
1 ACAT-GTCTTACACTAGCT
55135322 CACAATAGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
44 15 0.16
45 7 0.07
46 47 0.50
47 11 0.12
48 14 0.15
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (46 bp):
ACATGTCTTACACTAGCTTACATCTCGAGGCCGATGCATGTCCCAG
Found at i:55137896 original size:39 final size:39
Alignment explanation
Indices: 55137853--55137980 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
55137843 GGTCTTTAAC
** *
55137853 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
55137892 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
55137931 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
55137970 CCGGATATTTT
1 CCGGATATTTT
55137981 CAATCTCATA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:55141763 original size:45 final size:45
Alignment explanation
Indices: 55141714--55141804 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
55141704 TTTTCCCTTA
55141714 AACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTAATTAAT
1 AACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTAATTAAT
*
55141759 AACTTAGAAATTTGTCAAATTGCTATTTAAGACCTCCTAATTAAT
1 AACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTAATTAAT
55141804 A
1 A
55141805 TTTCAAAGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (45 bp):
AACTTAGAAATTGGTCAAATTGCTATTTAAGACCTCCTAATTAAT
Found at i:55148512 original size:40 final size:40
Alignment explanation
Indices: 55148364--55148550 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
55148354 TATTCGGATG
* *
55148364 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
55148404 A-ATTCCGGGCTAAG-CTCGAAGGCATTTGTGCGGGTTAGT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
55148443 AAAACTGGTCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
55148482 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
55148522 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
55148551 AGCAAGTAGC
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 63 0.49
40 65 0.51
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:55148583 original size:39 final size:40
Alignment explanation
Indices: 55148364--55148583 Score: 252
Period size: 39 Copynumber: 5.6 Consensus size: 40
55148354 TATTCGGATG
* *
55148364 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * ** *
55148404 A-ATTCCGGGCTAAG-CTCGAAGGCATTTGTGCGGGTTAGT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
55148443 AAAACTGGTCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
55148482 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
55148522 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-CT
* * *
55148562 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
55148584 TACTTGGTTT
Statistics
Matches: 156, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 79 0.51
40 77 0.49
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:55151625 original size:39 final size:40
Alignment explanation
Indices: 55151580--55151747 Score: 97
Period size: 40 Copynumber: 4.2 Consensus size: 40
55151570 CGGGGTTTAG
* * *
55151580 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
55151619 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * * **
55151659 CCGGATATAGTCGCTAGCACAAATGCCTTC-AGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
55151699 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
55151740 CCGGATAT
1 CCGGATAT
55151748 CATTCGAGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 17 0.16
40 61 0.57
41 27 0.25
42 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:55151738 original size:41 final size:40
Alignment explanation
Indices: 55151603--55151747 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
55151593 CTCGCACAAG
* * * * *
55151603 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
55151643 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * *
55151683 GCCTTC-AGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
55151724 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
55151748 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.02
40 59 0.66
41 27 0.30
42 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:55159406 original size:39 final size:39
Alignment explanation
Indices: 55159337--55159502 Score: 138
Period size: 40 Copynumber: 4.2 Consensus size: 39
55159327 CGGGGTTTAG
** * *
55159337 CCGGATATAACCACTCGCAC-AAGGCCTTCGGTCTTAAC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGTCTTAAC
* * * *
55159375 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTC-GGTCTTAAC
* **
55159415 CCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGG-TCTTAAC
* * * * *
55159455 CCGGATGTAGTGC-TTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGT-CACTAGCACAAATGCCTTC-GGTCTTAAC
55159495 CCGGATAT
1 CCGGATAT
55159503 CATTCGAGTA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
38 15 0.14
39 10 0.10
40 76 0.73
41 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (39 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGTCTTAAC
Found at i:55159421 original size:40 final size:38
Alignment explanation
Indices: 55159360--55159502 Score: 160
Period size: 40 Copynumber: 3.6 Consensus size: 38
55159350 CTCGCACAAG
* * * *
55159360 GCCTTCGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGACTTAGCCCGGATATAGTC-CTAGCACAAAT
55159399 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTC-CTAGCACAAAT
* * * *
55159439 GCCTTCGGATCTTAGTCCGGATGTAGTGCTTAGCACAAAA
1 GCCTTCGGA-CTTAGCCCGGATATAGT-CCTAGCACAAAT
55159479 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTC-GGACTTAGCCCGGATAT
55159503 CATTCGAGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 9 0.10
40 76 0.85
41 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (38 bp):
GCCTTCGGACTTAGCCCGGATATAGTCCTAGCACAAAT
Found at i:55160282 original size:13 final size:13
Alignment explanation
Indices: 55160261--55160308 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
55160251 ACTAAACATG
*
55160261 AACATAAATCCAA
1 AACACAAATCCAA
**
55160274 AACACAAAT-CTT
1 AACACAAATCCAA
*
55160286 AACATAAATCCAA
1 AACACAAATCCAA
55160299 AACACAAATC
1 AACACAAATC
55160309 TTACCTACCA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (13 bp):
AACACAAATCCAA
Found at i:55160295 original size:25 final size:25
Alignment explanation
Indices: 55160261--55160311 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
55160251 ACTAAACATG
55160261 AACATAAATCCAAAACACAAATCTT
1 AACATAAATCCAAAACACAAATCTT
55160286 AACATAAATCCAAAACACAAATCTT
1 AACATAAATCCAAAACACAAATCTT
55160311 A
1 A
55160312 CCTACCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (25 bp):
AACATAAATCCAAAACACAAATCTT
Found at i:55172790 original size:40 final size:40
Alignment explanation
Indices: 55172662--55172914 Score: 349
Period size: 40 Copynumber: 6.5 Consensus size: 40
55172652 AAGCCAAGTA
* * * * *
55172662 CCTTCGGGATTTA-ACCGGGTATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
55172701 CCTTC-GGACATAGCCCGGATATAGTAACT-GCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55172739 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55172779 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55172819 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
55172859 CCTTCGGGACTTAG-CCGGA-ACTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55172898 -CTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
55172915 TTATCATCCA
Statistics
Matches: 196, Mismatches: 12, Indels: 12
0.89 0.05 0.05
Matches are distributed among these distances:
38 32 0.16
39 63 0.32
40 101 0.52
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55180549 original size:77 final size:78
Alignment explanation
Indices: 55180420--55180667 Score: 308
Period size: 77 Copynumber: 3.2 Consensus size: 78
55180410 AAGCCAAGTA
* * * * * *
55180420 CCTTCGGGATTTAACCGGGTATAGCTACTCGCTCGAATGCCTTC-GGA-ATAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATATAGT
*
55180483 AACTCGCACAAATG
65 AACTAGCACAAATG
*
55180497 CCTTCGGGACTTAGCCGGATATAG-AACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
1 CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
55180561 ACTTGCACAAATG
66 ACTAGCACAAATG
* * * *
55180574 CCTTC-GGACTTAGCCTGGATATAGTAACTTGCACAATGCCTTCGGGACTTAGCTCGGA-ACAAG
1 CCTTCGGGACTTAGCC-GGATATAGCAACTCGCACAATGCCTTCGGGACTTAGCCCGGATA-TAG
*
55180637 TCACTAGCACAAATG
64 TAACTAGCACAAATG
55180652 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
55180668 CGGTTATCAT
Statistics
Matches: 151, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
75 8 0.05
76 20 0.13
77 63 0.42
78 50 0.33
79 10 0.07
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTAGCACAAATG
Found at i:55180583 original size:39 final size:40
Alignment explanation
Indices: 55180420--55180670 Score: 297
Period size: 39 Copynumber: 6.5 Consensus size: 40
55180410 AAGCCAAGTA
* * * * *
55180420 CCTTCGGGATTTA-ACCGGGTATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
55180459 CCTTC-GGA-ATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55180497 CCTTCGGGACTTAG-CCGGATATAG-AACTCGCACAAA-G
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55180534 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
55180574 CCTTC-GGACTTAGCCTGGATATAGTAACTTGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
55180612 CCTTCGGGACTTAGCTCGGA-ACAAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55180652 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55180671 TTATCATCCA
Statistics
Matches: 188, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
37 18 0.10
38 60 0.32
39 79 0.42
40 31 0.16
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55184656 original size:40 final size:40
Alignment explanation
Indices: 55184593--55184770 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
55184583 AAGCCAAGTA
* * * * *
55184593 CCTTCGGGATTTA-ACCGGGTATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * * *
55184632 CCTTCAGGACATAGCCTGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55184672 CCTTCGGGACTTAGCCCGGATATAGAAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55184712 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55184752 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55184771 TTATCATCCA
Statistics
Matches: 121, Mismatches: 16, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
39 11 0.09
40 110 0.91
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55192316 original size:40 final size:40
Alignment explanation
Indices: 55192246--55192503 Score: 378
Period size: 40 Copynumber: 6.5 Consensus size: 40
55192236 AAGCCAAGTA
* * * * *
55192246 CCTTCGGGATTTA-ACCGGGTATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
55192285 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55192325 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55192365 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55192405 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55192445 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55192485 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55192504 TTATCATACA
Statistics
Matches: 203, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 13 0.06
40 190 0.94
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55195053 original size:39 final size:40
Alignment explanation
Indices: 55194994--55195069 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
55194984 CGGATGATAA
*
55194994 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
55195034 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA
55195070 TAACTGCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:55195083 original size:24 final size:24
Alignment explanation
Indices: 55195051--55195097 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
55195041 AAGCCCGAAG
*
55195051 GCATTTGTGCGAGTTACTATAACT
1 GCATTTGTGCAAGTTACTATAACT
55195075 GCATTTGTGCAAGTTACTATAAC
1 GCATTTGTGCAAGTTACTATAAC
55195098 CGGGCTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
GCATTTGTGCAAGTTACTATAACT
Found at i:55195116 original size:103 final size:104
Alignment explanation
Indices: 55194990--55195177 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 104
55194980 TATTCGGATG
* * *
55194990 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAA-GCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTATA-ACCGGGCTAATGCCCGAAGGC
55195053 ATTTGTGCGAGTTACTATAACTGCATTTGTGCAAGTTACT
65 ATTTGTGCGAGTTACTATAACTGCATTTGTGCAAGTTACT
* *
55195093 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAACCGGGCTAATTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTATAACCGGGCTAATGCCCGAAGGCA
55195158 TTTGTGCGAGTTACTATAAC
66 TTTGTGCGAGTTACTATAAC
55195178 CGGGCTAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
103 47 0.60
104 31 0.40
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (104 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACTATAACCGGGCTAATGCCCGAAGGCA
TTTGTGCGAGTTACTATAACTGCATTTGTGCAAGTTACT
Found at i:55195128 original size:64 final size:63
Alignment explanation
Indices: 55195012--55195137 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 63
55195002 AGTCCCGAAG
* * *
55195012 GCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAACT
1 GCATTTGTGCAAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTATAACT
*
55195075 GCATTTGTGCAAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAAC
1 GCATTTGTGCAAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTATAAC
55195138 CGGGCTAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 2 0.04
63 26 0.46
64 29 0.51
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (63 bp):
GCATTTGTGCAAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTATAACT
Found at i:55195130 original size:40 final size:40
Alignment explanation
Indices: 55195075--55195201 Score: 227
Period size: 40 Copynumber: 3.2 Consensus size: 40
55195065 TACTATAACT
*
55195075 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
1 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
* *
55195115 GCATTTGTACGAGTTACTATAACCGGGCTAATTCCCGAAG
1 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
55195155 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
1 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
55195195 GCATTTG
1 GCATTTG
55195202 AGCAAGTAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (40 bp):
GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
Found at i:55195215 original size:40 final size:40
Alignment explanation
Indices: 55195075--55195234 Score: 209
Period size: 40 Copynumber: 4.0 Consensus size: 40
55195065 TACTATAACT
*
55195075 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
1 GCATTTGAGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
* *
55195115 GCATTTGTA-CGAGTTACTATAACCGGGCTAATTCCCGAAG
1 GCATTTG-AGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
* *
55195155 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAG
1 GCATTTGAGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
* * *
55195195 GCATTTGAGCAAG-TAGCTATATCC-GGCTAATTTCCGAAG
1 GCATTTGAGCAAGTTA-CTATAACCGGGCTAAGTCCCGAAG
55195234 G
1 G
55195235 TACTTGGTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
39 16 0.15
40 91 0.85
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (40 bp):
GCATTTGAGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
Found at i:55195215 original size:80 final size:79
Alignment explanation
Indices: 55195075--55195234 Score: 243
Period size: 80 Copynumber: 2.0 Consensus size: 79
55195065 TACTATAACT
*
55195075 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAACCG
1 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTACAAGTTACTATAACC-
55195140 GGCTAATTCCCGAAG
65 GGCTAATTCCCGAAG
* *
55195155 GCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG-AGCAAG-TAGCTATATC
1 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTA-CAAGTTA-CTATAAC
*
55195218 CGGCTAATTTCCGAAG
64 CGGCTAATTCCCGAAG
55195234 G
1 G
55195235 TACTTGGTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
79 18 0.24
80 56 0.76
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (79 bp):
GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTACAAGTTACTATAACCG
GCTAATTCCCGAAG
Found at i:55198614 original size:46 final size:43
Alignment explanation
Indices: 55198493--55198619 Score: 130
Period size: 46 Copynumber: 2.8 Consensus size: 43
55198483 TAGGATAGGA
**
55198493 AGCCGATGCCATGTCCCAGGTATGGTCTTACACTAGCTTAATTCGT
1 AGCCGATG-CATGT-CCAGACAT-GTCTTACACTAGCTTAATTCGT
* *
55198539 AGCCGATGCATGTCTAGACATGTCTTACACTGGCTTACATCTCG-
1 AGCCGATGCATGTCCAGACATGTCTTACACTAGCTTA-AT-TCGT
* *
55198583 AGGCTGATGCATGTCCCAGACGTGTCTTACACTAGCT
1 A-GCCGATGCATGT-CCAGACATGTCTTACACTAGCT
55198620 CTCGTCTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
43 15 0.22
44 8 0.12
45 19 0.28
46 27 0.39
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (43 bp):
AGCCGATGCATGTCCAGACATGTCTTACACTAGCTTAATTCGT
Found at i:55204286 original size:25 final size:27
Alignment explanation
Indices: 55204253--55204307 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
55204243 CTTATGAGCA
*
55204253 TCCCAATTAAA-GGTTCTTTGTGAACT
1 TCCCAATTAAATGGCTCTTTGTGAACT
*
55204279 TCCC-ATTAAATTGGCTCTTTGTGAGCT
1 TCCCAATTAAA-TGGCTCTTTGTGAACT
55204306 TC
1 TC
55204308 TCGATAGTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 4 0.16
27 15 0.60
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (27 bp):
TCCCAATTAAATGGCTCTTTGTGAACT
Found at i:55204481 original size:24 final size:23
Alignment explanation
Indices: 55204433--55204486 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
55204423 TTACCAGATA
*
55204433 AGCTTCCTGATAGGCTCCTTATG
1 AGCTTCCTGAAAGGCTCCTTATG
*
55204456 AGCTTCCTGAAATGGCT-CTATGTG
1 AGCTTCCTGAAA-GGCTCCT-TATG
55204480 AGCTTCC
1 AGCTTCC
55204487 CGTTACAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (23 bp):
AGCTTCCTGAAAGGCTCCTTATG
Found at i:55209491 original size:52 final size:53
Alignment explanation
Indices: 55209423--55209522 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 53
55209413 GTAAATTCTT
* *
55209423 TTTTTATAGGATAAAAACCAACAGCCTAAGATTATCTTCTCCT-TTTTATATA
1 TTTTTATAGGATAAAAACCAACAACCCAAGATTATCTTCTCCTCTTTTATATA
* *
55209475 TTTTTCTAGGATAAAAACCAATAACCCAAGATTATCTTCTCCTCTTTT
1 TTTTTATAGGATAAAAACCAACAACCCAAGATTATCTTCTCCTCTTTT
55209523 TTAGGTAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (53 bp):
TTTTTATAGGATAAAAACCAACAACCCAAGATTATCTTCTCCTCTTTTATATA
Found at i:55221833 original size:54 final size:54
Alignment explanation
Indices: 55221751--55221858 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
55221741 CGAATCAGCT
55221751 GTATACCTTTTTGCCCGAAATTACGTATATACATATATATACATATATACACTA
1 GTATACCTTTTTGCCCGAAATTACGTATATACATATATATACATATATACACTA
55221805 GTATACCTTTTTGCCCGAAATTACGTATATACATATATATACATATATACACTA
1 GTATACCTTTTTGCCCGAAATTACGTATATACATATATATACATATATACACTA
55221859 ACATACAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (54 bp):
GTATACCTTTTTGCCCGAAATTACGTATATACATATATATACATATATACACTA
Found at i:55222266 original size:39 final size:39
Alignment explanation
Indices: 55222223--55222341 Score: 166
Period size: 39 Copynumber: 3.1 Consensus size: 39
55222213 GTCCAGCAGG
* *
55222223 TAGCCTGCGGACCTAAAGTCCGGATATAACTCTCGCATA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
* * *
55222262 TAGCCTGCGGACATGAAGTCTGGATATAATTCTCGCTTA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
* * *
55222301 TAGCTTACGGACCTGAAGTCCGGATATAATTCTCACATA
1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
55222340 TA
1 TA
55222342 TATATTCACA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (39 bp):
TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
Found at i:55225941 original size:28 final size:28
Alignment explanation
Indices: 55225899--55225971 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
55225889 TGAAACACAC
* *
55225899 TTCGCATACACAGTGCCT-ACTGACTGAT
1 TTCGCACACATAGTGCCTAACT-ACTGAT
55225927 TTCGCACACATAGTGCCTCAACTACTGAT
1 TTCGCACACATAGTGCCT-AACTACTGAT
* *
55225956 CTGGCACACATAGTGC
1 TTCGCACACATAGTGC
55225972 TCGGTTGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 16 0.41
29 20 0.51
30 3 0.08
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (28 bp):
TTCGCACACATAGTGCCTAACTACTGAT
Found at i:55226081 original size:40 final size:40
Alignment explanation
Indices: 55226009--55226164 Score: 253
Period size: 40 Copynumber: 3.9 Consensus size: 40
55225999 CCTCATAATT
* * *
55226009 CCAGCACGAATGC-CTTCGAGG-TTTAGCACGGATATATCA
1 CCAGCACGAATGCTCTTCG-GGACTTAGCCCGGATATAACA
*
55226048 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
55226088 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
55226128 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
55226165 TAACTCTCAA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 14 0.13
40 96 0.87
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACA
Found at i:55228326 original size:39 final size:39
Alignment explanation
Indices: 55228219--55228337 Score: 157
Period size: 39 Copynumber: 3.1 Consensus size: 39
55228209 GTCTAGCAAG
* *
55228219 TAGCCTGCGGACCTAAAGTCCGGATATAACTCTCGCATA
1 TAGCCTACGGACCTAAAGTCCGGATATAATTCTCGCATA
* * *
55228258 TAGCCTGCGGACATAAAGTCCGGATATAATTCTCGCTTA
1 TAGCCTACGGACCTAAAGTCCGGATATAATTCTCGCATA
* * * *
55228297 TAGCTTACGGACCTGAAGTCTGGATATAATTCTCACATA
1 TAGCCTACGGACCTAAAGTCCGGATATAATTCTCGCATA
55228336 TA
1 TA
55228338 TATATTCACA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (39 bp):
TAGCCTACGGACCTAAAGTCCGGATATAATTCTCGCATA
Found at i:55232064 original size:21 final size:21
Alignment explanation
Indices: 55232038--55232079 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55232028 CGTCACGAAG
*
55232038 AAAGATGGATCCGTGAGACTT
1 AAAGATGAATCCGTGAGACTT
55232059 AAAGATGAATCCGTGAGACTT
1 AAAGATGAATCCGTGAGACTT
55232080 TGTATTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (21 bp):
AAAGATGAATCCGTGAGACTT
Found at i:55238489 original size:21 final size:22
Alignment explanation
Indices: 55238465--55238510 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55238455 AACACGAGCC
*
55238465 TGTCCCATGG-TCACACAGGTG
1 TGTCCCATGGACCACACAGGTG
* *
55238486 TGTCCCTTGGACCACACGGGTG
1 TGTCCCATGGACCACACAGGTG
55238508 TGT
1 TGT
55238511 GAGCCCTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.26
Consensus pattern (22 bp):
TGTCCCATGGACCACACAGGTG
Found at i:55240643 original size:30 final size:29
Alignment explanation
Indices: 55240578--55240894 Score: 86
Period size: 29 Copynumber: 10.9 Consensus size: 29
55240568 GAGTACTAAA
* * *
55240578 CGATGGTTGTAACCATCCATTTTCATATT
1 CGATGGTCGAAACCATCCATTTTCATAAT
*
55240607 CAATGGTCGAAACCATCCCA-TTTCATTAAT
1 CGATGGTCGAAACCAT-CCATTTTCA-TAAT
*** * * *
55240637 CGATGGTCGTCGCCATCCTTTTTTATAGT
1 CGATGGTCGAAACCATCCATTTTCATAAT
** * ** *
55240666 TAATGGTTGTCACCATCCGTTTTCATAAT
1 CGATGGTCGAAACCATCCATTTTCATAAT
* * * * * *
55240695 CGATAGCCGAAGCTATCCTTTTTCATATT
1 CGATGGTCGAAACCATCCATTTTCATAAT
* * * * * ** * *
55240724 CTATAGCCGAAGCTATCCCCTTTCGTATT
1 CGATGGTCGAAACCATCCATTTTCATAAT
** * *
55240753 CGATGG-CGTCACCATCCCTTTTCATAGT
1 CGATGGTCGAAACCATCCATTTTCATAAT
* * * * *
55240781 TGATGGTC-ATCACCATCCCTGTTCATCA-
1 CGATGGTCGA-AACCATCCATTTTCATAAT
* * * *
55240809 CTGATAG-CTGAAGCTATCCCTTTTCATAAT
1 C-GATGGTC-GAAACCATCCATTTTCATAAT
* * * *
55240839 CGATAGTCGAAGCTATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCATTTTCATAAT
* * * *
55240868 CGATAGTCGAAGCTATCCCTTTTCATA
1 CGATGGTCGAAACCATCCATTTTCATA
55240895 TTCAATGATC
Statistics
Matches: 224, Mismatches: 54, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
28 21 0.09
29 178 0.79
30 25 0.11
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCATTTTCATAAT
Found at i:55240712 original size:29 final size:29
Alignment explanation
Indices: 55240680--55240894 Score: 179
Period size: 29 Copynumber: 7.4 Consensus size: 29
55240670 GGTTGTCACC
*
55240680 ATCCGTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * *
55240709 ATCCTTTTTCATATTCTATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * * *
55240738 ATCCCCTTTCGTATTCGAT-GGCGTCA-CC
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
* * * * *
55240766 ATCCCTTTTCATAGTTGATGGTC-ATCA-CC
1 ATCCCTTTTCATAATCGATAGCCGA--AGCT
* * *
55240795 ATCCCTGTTCATCA-CTGATAGCTGAAGCT
1 ATCCCTTTTCATAATC-GATAGCCGAAGCT
*
55240824 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
*
55240853 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
55240882 ATCCCTTTTCATA
1 ATCCCTTTTCATA
55240895 TTCAATGATC
Statistics
Matches: 150, Mismatches: 28, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
28 20 0.13
29 128 0.85
30 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:55240806 original size:115 final size:116
Alignment explanation
Indices: 55240621--55240894 Score: 311
Period size: 115 Copynumber: 2.4 Consensus size: 116
55240611 GGTCGAAACC
* * * * ** *
55240621 ATCCCATTTCATTAATCGATGGTCGTCGCCATCCTTTTTTATAGTTAATGGTTGTCACCATCCGT
1 ATCCCCTTTCA-TAATCGATGGTCGTCACCATCCCTTTTCATAGTTAATGGTCATCACCATCCCT
* * * *
55240686 TTTCATAA-TCGATAGCCGAAGCTATCCTTTTTCATATTCTATAGCCGAAGCT
65 GTTCATAACT-GATAGCCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
* * *
55240738 ATCCCCTTTCGTATTCGATGG-CGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTG
1 ATCCCCTTTCATAATCGATGGTCGTCACCATCCCTTTTCATAGTTAATGGTCATCACCATCCCTG
* * *
55240802 TTCATCACTGATAGCTGAAGCTATCCCTTTTCATAATCGATAGTCGAAGCT
66 TTCATAACTGATAGCCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
* * * *
55240853 ATCCCTTTTCATAATCGATAGTCG-AAGCTATCCCTTTTCATA
1 ATCCCCTTTCATAATCGATGGTCGTCA-CCATCCCTTTTCATA
55240895 TTCAATGATC
Statistics
Matches: 131, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
115 96 0.73
116 26 0.20
117 9 0.07
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.36
Consensus pattern (116 bp):
ATCCCCTTTCATAATCGATGGTCGTCACCATCCCTTTTCATAGTTAATGGTCATCACCATCCCTG
TTCATAACTGATAGCCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:55241411 original size:18 final size:19
Alignment explanation
Indices: 55241370--55241411 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55241360 TCATAAAAAA
*
55241370 TCAAATAACAAAATACTTT
1 TCAAATAACAAAATAATTT
*
55241389 T-AAATATC-AAATAATTT
1 TCAAATAACAAAATAATTT
55241406 TCAAAT
1 TCAAAT
55241412 TCATCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAAATAACAAAATAATTT
Found at i:55248432 original size:40 final size:40
Alignment explanation
Indices: 55248343--55248565 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
55248333 TTGAATGATG
* * * *
55248343 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
55248383 T-CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
55248422 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55248460 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55248500 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55248541 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55248566 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 25 0.15
39 41 0.25
40 95 0.58
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55248477 original size:78 final size:79
Alignment explanation
Indices: 55248343--55248565 Score: 283
Period size: 78 Copynumber: 2.8 Consensus size: 79
55248333 TTGAATGATG
* * * * * *
55248343 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAT-CGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
55248406 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
*
55248422 TCCGGGCTAAG-CCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
*
55248486 TGCGAGTTACTAAA
66 TGCGAGATACTAAA
* *
55248500 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
55248564 TG
64 TG
55248566 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
77 9 0.07
78 57 0.45
79 21 0.17
80 38 0.30
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:55248583 original size:80 final size:79
Alignment explanation
Indices: 55248343--55248598 Score: 238
Period size: 78 Copynumber: 3.3 Consensus size: 79
55248333 TTGAATGATG
* * * * * * *
55248343 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAT-CGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATT
** *
55248406 TGTGCGAGAT-ACTAAT
64 TGAACGAG-TGACTAAA
* *
55248422 TCCGGGCTAAG-CCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
** *
55248486 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
55248500 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
55248564 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
55248580 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55248599 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
77 10 0.07
78 56 0.37
79 36 0.24
80 49 0.32
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:55399901 original size:40 final size:39
Alignment explanation
Indices: 55399804--55400013 Score: 210
Period size: 40 Copynumber: 5.3 Consensus size: 39
55399794 TCTTCGGAAT
* * *
55399804 TTAG-CCGGATATAACCACAAGCACAATTGCCTTC-GGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
* * * *
55399842 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
*
55399882 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * * *
55399922 TTAGCCCGGATAAAATCACTAGAATAAATGCCTT-GGGGC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
55399961 TTAGCCCGGATAAAATCACAAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
55400001 TTAGCCCGGATAT
1 TTAGCCCGGATAT
55400014 CATTCAAATG
Statistics
Matches: 149, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 5 0.03
39 59 0.40
40 81 0.54
41 4 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:55412761 original size:46 final size:46
Alignment explanation
Indices: 55412618--55412783 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
55412608 ATTGTGAGCT
* * *
55412618 AGTGTAAGACATGTCT-GGACATGCATCAGCCAC-ATTAAGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA--AAGATAAGCC
* * * * *
55412663 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTG--AGATGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAAAGAT-A-AGCC
*
55412711 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAACATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAAGATAAGCC
55412757 AGTGTAAGACATGTCTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
55412784 TGGCAATGAG
Statistics
Matches: 98, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
45 12 0.12
46 45 0.46
47 20 0.20
48 21 0.21
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAAGATAAGCC
Found at i:55412776 original size:93 final size:90
Alignment explanation
Indices: 55412615--55412825 Score: 250
Period size: 93 Copynumber: 2.3 Consensus size: 90
55412605 GTTATTGTGA
* * *
55412615 GCTAGTGTAAGACATGTCT-GGACATGCATCAGCCACATTAAGAGAGCCAGTGTAAGACCATGTT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACA-TAACAAAGCCAGTGTAAGACCATGTC
*
55412679 TGGGACATGGCATCGGCATTGAGATGAGT
65 TGGGACAT-GCATCGGCAATGAGA-G-GT
* *
55412708 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-AACATAAGCCAGTGTAAGA-CATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATAACA-AAGCCAGTGTAAGACCATGT
*
55412771 CTGGGACATGCATTGGCAATGAGAGGT
64 CTGGGACATGCATCGGCAATGAGAGGT
*
55412798 G-TCAGTGTAAGACCATGTTTGGGACATG
1 GCT-AGTGTAAGA-CATGTCTGGGACATG
55412826 GCATTGACAA
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
89 1 0.01
90 12 0.11
91 15 0.14
92 13 0.12
93 35 0.33
94 28 0.27
95 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (90 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATAACAAAGCCAGTGTAAGACCATGTCT
GGGACATGCATCGGCAATGAGAGGT
Found at i:55420393 original size:27 final size:26
Alignment explanation
Indices: 55420345--55420404 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
55420335 GCGAGGCTGC
*
55420345 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55420372 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
55420398 CATATAT
1 CAGATAT
55420405 ATATAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55421141 original size:27 final size:27
Alignment explanation
Indices: 55421111--55421255 Score: 177
Period size: 27 Copynumber: 5.3 Consensus size: 27
55421101 AAGGTAAAAT
* * *
55421111 GGTAGTTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
55421138 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
55421165 GGT-GTTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
55421192 GGTAATTCTT-CCCTACAGGGGTATTTC
1 GGTAATT-TTACCCTACAAGGGTATTTC
*
55421219 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
55421246 GGTATATTTT
1 GGTA-ATTTT
55421256 TAAATCGAGG
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.03
27 89 0.89
28 7 0.07
29 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:55421206 original size:54 final size:54
Alignment explanation
Indices: 55421115--55421249 Score: 218
Period size: 54 Copynumber: 2.5 Consensus size: 54
55421105 TAAAATGGTA
* *
55421115 GTTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGT
1 GTTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
*
55421168 GTTTCTACCCTACAAGGGTATTTCGGTAATTCTTCCCTACAGGGGTATTTCGGT
1 GTTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
**
55421222 AATTCTACCCTACAAGGGTATTTCGGTA
1 GTTTCTACCCTACAAGGGTATTTCGGTA
55421250 TATTTTTAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 4 0.05
54 72 0.95
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (54 bp):
GTTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
Found at i:55421266 original size:27 final size:27
Alignment explanation
Indices: 55421210--55421420 Score: 111
Period size: 27 Copynumber: 7.9 Consensus size: 27
55421200 TTCCCTACAG
* ** *
55421210 GGGTATTTCGGTAA-TTCTACCCTACAA
1 GGGTATTTCGGTAATTTTTACAAT-CGA
55421237 GGGTATTTCGGTATATTTTTA-AATCGA
1 GGGTATTTCGGTA-ATTTTTACAATCGA
*** * *
55421264 GGGTACAACGGTAATTCTGTA-AATTGA
1 GGGTATTTCGGTAATT-TTTACAATCGA
55421291 GGGTAATTT-GGTAA-TTTTACAAGTCGA
1 GGGT-ATTTCGGTAATTTTTACAA-TCGA
* *
55421318 GGGTATTTCAGTAA-TTTTACAGGTCGA
1 GGGTATTTCGGTAATTTTTACA-ATCGA
* *
55421345 GGGTATTTCAGTAA-TTTCACAAATC-A
1 GGGTATTTCGGTAATTTTTAC-AATCGA
* *
55421371 GGGGTATTTTGGTAA-TTTTACAAACTTG-
1 -GGGTATTTCGGTAATTTTTAC-AA-TCGA
*
55421399 GGGTATTTTGGTAA-TTTTACAA
1 GGGTATTTCGGTAATTTTTACAA
55421421 ACCAAGGGTA
Statistics
Matches: 150, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.02
26 13 0.09
27 125 0.83
28 5 0.03
29 4 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTTACAATCGA
Found at i:55421276 original size:54 final size:54
Alignment explanation
Indices: 55421119--55421281 Score: 134
Period size: 54 Copynumber: 3.0 Consensus size: 54
55421109 ATGGTAGTTT
* * ** *** **
55421119 TACCCCACAAGGGTATCTCGGTAATTC-TACCCTACAGGGGTATTTCGGTGTTTC
1 TACCCTACAAGGGTATTTCGGTAATTCTTA-AATACAGGGGTACAACGGTAATTC
*** ***
55421173 TACCCTACAAGGGTATTTCGGTAATTCTTCCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTCTTAAATACAGGGGTACAACGGTAATTC
*
55421227 TACCCTACAAGGGTATTTCGGTATATTTTTAAAT-C-GAGGGTACAACGGTAATTC
1 TACCCTACAAGGGTATTTCGGTA-ATTCTTAAATACAG-GGGTACAACGGTAATTC
55421281 T
1 T
55421282 GTAAATTGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 86 0.91
55 7 0.07
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (54 bp):
TACCCTACAAGGGTATTTCGGTAATTCTTAAATACAGGGGTACAACGGTAATTC
Found at i:55421276 original size:81 final size:81
Alignment explanation
Indices: 55421129--55421281 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
55421119 TACCCCACAA
* * ** ***
55421129 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTGTTTCTACCCTACAAGGGTATTTCGG
1 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAAGGGTACAACGG
55421194 TAATTCTTCCCTACAG
66 TAATTCTTCCCTACAG
* * *
55421210 GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTATATTTTTA-AAT-CGAGGGTACAAC
1 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCGG--TATTTCTACAATACAAGGGTACAAC
55421273 GGTAATTCT
64 GGTAATTCT
55421282 GTAAATTGAG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 53 0.88
82 1 0.02
83 6 0.10
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (81 bp):
GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAAGGGTACAACGG
TAATTCTTCCCTACAG
Found at i:55421347 original size:54 final size:54
Alignment explanation
Indices: 55421289--55421440 Score: 157
Period size: 54 Copynumber: 2.8 Consensus size: 54
55421279 TCTGTAAATT
* * **
55421289 GAGGGTAATTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTAC-AGGTC
1 GAGGGTAATTTGGTAATTTTACAAATC-AGGGTATTTTAGTAATTTTACAAACTC
* * * *
55421343 GAGGGT-ATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTT
1 GAGGGTAATTT-GGTAATTTTACAAATCA-GGGTATTTTAGTAATTTTACAAACTC
* *
55421398 G-GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAAT
1 GAGGGTAATTTGGTAATTTTACAAATC-AGGGTATTTTAGTAAT
55421441 ACTAGCTTAC
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
53 5 0.06
54 68 0.85
55 7 0.09
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (54 bp):
GAGGGTAATTTGGTAATTTTACAAATCAGGGTATTTTAGTAATTTTACAAACTC
Found at i:55421421 original size:27 final size:27
Alignment explanation
Indices: 55421291--55421440 Score: 117
Period size: 27 Copynumber: 5.6 Consensus size: 27
55421281 TGTAAATTGA
* * * *
55421291 GGGTAATTTGGTAATTTTAC-AAGTCG
1 GGGTATTTTAGTAATTTTACAAACTAG
* ** *
55421317 AGGGTATTTCAGTAATTTTAC-AGGTCG
1 -GGGTATTTTAGTAATTTTACAAACTAG
* *
55421344 AGGGTATTTCAGTAATTTCACAAA-TCAG
1 -GGGTATTTTAGTAATTTTACAAACT-AG
* *
55421372 GGGTATTTTGGTAATTTTACAAACTTG
1 GGGTATTTTAGTAATTTTACAAACTAG
* * *
55421399 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTAGTAATTTTACAAACTAG
55421426 GGGTATTTTAGTAAT
1 GGGTATTTTAGTAAT
55421441 ACTAGCTTAC
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 102 0.97
28 3 0.03
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAACTAG
Found at i:55421429 original size:81 final size:81
Alignment explanation
Indices: 55421291--55421440 Score: 194
Period size: 81 Copynumber: 1.9 Consensus size: 81
55421281 TGTAAATTGA
* *** *
55421291 GGGTAATTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTACAGGTCGAGGGTATTTCAG
1 GGGTAATTTGGTAATTTTACAACTCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCAG
55421356 TAATTTCACAAATCAG
66 TAATTTCACAAATCAG
* * ** *
55421372 GGGTATTTTGGTAATTTTACAAACTTG-GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTA
1 GGGTAATTTGGTAATTTTAC-AACTCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCA
55421436 GTAAT
65 GTAAT
55421441 ACTAGCTTAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 54 0.93
82 4 0.07
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (81 bp):
GGGTAATTTGGTAATTTTACAACTCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCAG
TAATTTCACAAATCAG
Found at i:55443686 original size:20 final size:20
Alignment explanation
Indices: 55443661--55443705 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
55443651 ATGGACTAAA
*
55443661 ATGAAAAGTT-GTAAATTTT
1 ATGAAAAATTCGTAAATTTT
*
55443680 GATGAAAAATTCTTAAATTTT
1 -ATGAAAAATTCGTAAATTTT
55443701 ATGAA
1 ATGAA
55443706 TACATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGAAAAATTCGTAAATTTT
Found at i:55444999 original size:24 final size:24
Alignment explanation
Indices: 55444954--55445000 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55444944 TTTAGAGAAT
*
55444954 TTTGTGTTTACGTTTTGAGGGTTC
1 TTTGTGTTTACGTTTTCAGGGTTC
* * *
55444978 TTTGTTTTTAGGTTTTCTGGGTT
1 TTTGTGTTTACGTTTTCAGGGTT
55445001 TAGTTTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.28, T:0.60
Consensus pattern (24 bp):
TTTGTGTTTACGTTTTCAGGGTTC
Found at i:55447922 original size:12 final size:12
Alignment explanation
Indices: 55447905--55447931 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55447895 ATTCCGAAGT
55447905 ATATATATATAC
1 ATATATATATAC
55447917 ATATATATATAC
1 ATATATATATAC
55447929 ATA
1 ATA
55447932 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:55448462 original size:27 final size:28
Alignment explanation
Indices: 55448378--55448475 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
55448368 CATGAGATTG
* * * *
55448378 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
55448407 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
55448435 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55448462 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
55448476 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55448486 original size:27 final size:27
Alignment explanation
Indices: 55448406--55448488 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
55448396 TAAATTGTAC
* *
55448406 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55448434 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55448461 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55448488 A
1 A
55448489 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55456192 original size:12 final size:12
Alignment explanation
Indices: 55456175--55456201 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55456165 ATTCCGAAGT
55456175 ATATATATATAC
1 ATATATATATAC
55456187 ATATATATATAC
1 ATATATATATAC
55456199 ATA
1 ATA
55456202 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:55456732 original size:27 final size:28
Alignment explanation
Indices: 55456648--55456745 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
55456638 CATGAGATTG
* * * *
55456648 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
55456677 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
55456705 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55456732 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
55456746 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55456756 original size:27 final size:27
Alignment explanation
Indices: 55456676--55456758 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
55456666 TAAATTGTAC
* *
55456676 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55456704 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55456731 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55456758 A
1 A
55456759 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55463931 original size:46 final size:46
Alignment explanation
Indices: 55463878--55463976 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
55463868 TGTGAATTGC
* *
55463878 ATAAATGTTTAATGTATGAAATTAATCATGTACTTGATATTGTTAA
1 ATAAATGTTTAATGTATGAAATTAATCATGTACTCGATATTATTAA
55463924 ATAAATGTTTAATGTATGAAATTAATCATGTACTCGATATTATTAA
1 ATAAATGTTTAATGTATGAAATTAATCATGTACTCGATATTATTAA
55463970 ATAAATG
1 ATAAATG
55463977 ATAAGTCCCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (46 bp):
ATAAATGTTTAATGTATGAAATTAATCATGTACTCGATATTATTAA
Found at i:55463954 original size:23 final size:23
Alignment explanation
Indices: 55463882--55463954 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
55463872 AATTGCATAA
55463882 ATGTTTAATGTATGAAATTAATC
1 ATGTTTAATGTATGAAATTAATC
55463905 ATGTACTTGATATTGT-T-AAA-TAA--
1 ATGT--TT-A-A-TGTATGAAATTAATC
55463928 ATGTTTAATGTATGAAATTAATC
1 ATGTTTAATGTATGAAATTAATC
55463951 ATGT
1 ATGT
55463955 ACTCGATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 20
0.67 0.00 0.33
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 4 0.10
21 5 0.12
23 12 0.30
25 5 0.12
26 4 0.10
27 2 0.05
28 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (23 bp):
ATGTTTAATGTATGAAATTAATC
Found at i:55472492 original size:14 final size:14
Alignment explanation
Indices: 55472470--55472500 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55472460 AAAAAATAGT
*
55472470 CCGATTGAACCGAA
1 CCGAGTGAACCGAA
55472484 CCGAGTGAACCGAA
1 CCGAGTGAACCGAA
55472498 CCG
1 CCG
55472501 GCCAAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.10
Consensus pattern (14 bp):
CCGAGTGAACCGAA
Found at i:55481917 original size:29 final size:29
Alignment explanation
Indices: 55481884--55481943 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
55481874 ATTAAATGAG
55481884 ATAGAATAGAAATAATGGATGAATTGTGA
1 ATAGAATAGAAATAATGGATGAATTGTGA
55481913 ATAGAATAGAAATAATGGATGAATTGTGA
1 ATAGAATAGAAATAATGGATGAATTGTGA
55481942 AT
1 AT
55481944 TGCTAAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.28
Consensus pattern (29 bp):
ATAGAATAGAAATAATGGATGAATTGTGA
Found at i:55484215 original size:40 final size:40
Alignment explanation
Indices: 55484119--55484256 Score: 161
Period size: 40 Copynumber: 3.4 Consensus size: 40
55484109 AGAACAATTC
* * * * *
55484119 CGCACACTTAGTGCCATCTCAATTACCCAATGCTAAGTTGATAT
1 CGCACACTTAGTGCC-TCAC-A-TAGCCAAAGCT-AGTTTAAAT
* *
55484163 CGCACACTTAGTGCCTCAGATAGCCGAAGCTAGTTTAAAT
1 CGCACACTTAGTGCCTCACATAGCCAAAGCTAGTTTAAAT
55484203 CGCACACTTAGTGCCTCACATAGCCAAAGCTAGTTTAAAT
1 CGCACACTTAGTGCCTCACATAGCCAAAGCTAGTTTAAAT
55484243 CGCACA-TATAGTGC
1 CGCACACT-TAGTGC
55484257 GAAATACTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 57 0.68
41 8 0.10
42 1 0.01
43 2 0.02
44 15 0.18
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (40 bp):
CGCACACTTAGTGCCTCACATAGCCAAAGCTAGTTTAAAT
Found at i:55488552 original size:46 final size:45
Alignment explanation
Indices: 55488485--55488659 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
55488475 TATTTGGGCA
* *
55488485 TCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGTATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCGAA-G
*** *
55488531 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGT-A-T-GCGAAG
* * *
55488578 TCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCGAA-G
* *
55488624 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
55488660 GGCGGGTTAC
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCGAAG
Found at i:55488640 original size:93 final size:93
Alignment explanation
Indices: 55488481--55488653 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
55488471 AGGATATTTG
** * * *
55488481 GGCATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGTATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55488546 TTGAGTCCGAGTTCAAGAGATGTAACTA
66 TTGAGTCCGAGTTCAAGAGATGTAACTA
* * *
55488574 GGCATCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55488639 TTGAGTCCGAGTTCA
66 TTGAGTCCGAGTTCA
55488654 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCAAGAGATGTAACTA
Found at i:55508856 original size:40 final size:40
Alignment explanation
Indices: 55508812--55508892 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
55508802 ATTCTATTTG
* * *
55508812 ATTCAGAGTTATCAG-AGTATAAATAGAGGCACATAAGTGC
1 ATTCAGAGGTA-CAGAAGTACAAACAGAGGCACATAAGTGC
* * *
55508852 ATTCAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGC
1 ATTCAGAGGTACAGAAGTACAAACAGAGGCACATAAGTGC
55508892 A
1 A
55508893 ATCAAGGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (40 bp):
ATTCAGAGGTACAGAAGTACAAACAGAGGCACATAAGTGC
Found at i:55508889 original size:20 final size:20
Alignment explanation
Indices: 55508866--55508904 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55508856 AGGGGTACCG
*
55508866 AAGTACAAACAGGGGCACAT
1 AAGTACAAACAAGGGCACAT
* *
55508886 AAGTGCAATCAAGGGCACA
1 AAGTACAAACAAGGGCACA
55508905 AACAGGAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.10
Consensus pattern (20 bp):
AAGTACAAACAAGGGCACAT
Found at i:55509831 original size:5 final size:5
Alignment explanation
Indices: 55509823--55509856 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
55509813 AAATAAAAAA
55509823 TTATT TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTAT
55509857 GATTGGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:55512593 original size:16 final size:15
Alignment explanation
Indices: 55512567--55512617 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
55512557 TTTTTCATCT
55512567 TTTACTTAATTAACA
1 TTTACTTAATTAACA
*
55512582 TTTACGTTAATTATCA
1 TTTAC-TTAATTAACA
* *
55512598 TACTACTTAATTAACC
1 T-TTACTTAATTAACA
55512614 TTTA
1 TTTA
55512618 AAAATTATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 7 0.24
16 19 0.66
17 3 0.10
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (15 bp):
TTTACTTAATTAACA
Found at i:55514313 original size:45 final size:45
Alignment explanation
Indices: 55514264--55514426 Score: 174
Period size: 45 Copynumber: 3.7 Consensus size: 45
55514254 TATGTTTTTT
*
55514264 CGTGTGAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
* * * * *
55514309 CGTGTAAGACCATGTCTAGGACATCGTCATCG-TAT-T-TGATT-
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
* *** *
55514350 CGTGTTAGACCGCATCTGGGATGTTGGCATCGATATATGTGGTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
*
55514395 CGTGTAAGACCCTGTCTGGGACAG-TGGCATCG
1 CGTGTAAGACCATGTCTGGGAC-GTTGGCATCG
55514427 TTATGAGGTA
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 23 0.25
42 7 0.08
43 2 0.02
44 7 0.08
45 52 0.57
46 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (45 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
Found at i:55523422 original size:107 final size:107
Alignment explanation
Indices: 55523228--55523443 Score: 387
Period size: 107 Copynumber: 2.0 Consensus size: 107
55523218 TTACTGGTTC
* **
55523228 CACTGTTTATTACCGAATGTCTTATGAACAGATAGAGTTTCAGAGTTATTTTCGCGCAATCACAA
1 CACTATTTATTACCGAATGTCTTATGAACAGATAGAGTTTCAGAGTTATTTTCAAGCAATCACAA
* *
55523293 TTTAGCTACGGTCCCAGTTTTGTAGCCCTAATACTACATTAT
66 TTTAGCTACAGTCCCAGCTTTGTAGCCCTAATACTACATTAT
55523335 CACTATTTATTACCGAATGTCTTATGAACAGATAGAGTTTCAGAGTTATTTTCAAGCAATCACAA
1 CACTATTTATTACCGAATGTCTTATGAACAGATAGAGTTTCAGAGTTATTTTCAAGCAATCACAA
55523400 TTTAGCTACAGTCCCAGCTTTGTAGCCCTAATACTACATTAT
66 TTTAGCTACAGTCCCAGCTTTGTAGCCCTAATACTACATTAT
55523442 CA
1 CA
55523444 ATAGCACTAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (107 bp):
CACTATTTATTACCGAATGTCTTATGAACAGATAGAGTTTCAGAGTTATTTTCAAGCAATCACAA
TTTAGCTACAGTCCCAGCTTTGTAGCCCTAATACTACATTAT
Found at i:55526657 original size:43 final size:43
Alignment explanation
Indices: 55526594--55526679 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
55526584 TATGTGATTC
*
55526594 CGATATGTGTTTACGAGTAAGACC-CTGTCTAGGACAG-TGGCAT
1 CGATATGTGGTTACGAGTAAGACCAC-GTCTAGGAC-GTTGGCAT
55526637 CGATATGTGGTTAC-ATGTAAGACCACGTCTAGGACGTTGGCAT
1 CGATATGTGGTTACGA-GTAAGACCACGTCTAGGACGTTGGCAT
55526680 TGTACGATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 2 0.05
43 36 0.92
44 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CGATATGTGGTTACGAGTAAGACCACGTCTAGGACGTTGGCAT
Found at i:55533137 original size:27 final size:27
Alignment explanation
Indices: 55533107--55533425 Score: 295
Period size: 27 Copynumber: 11.8 Consensus size: 27
55533097 ATGCCCTCAA
* *
55533107 TTTGTAAAATTACTAAAATACCTCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
*
55533134 TTTGTAAAATTACCAAAATACCCCTGG
1 TTTGTAAAATTACCAAAATACCCCTAG
*
55533161 TTTATAAAATTACCAAAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
* *
55533188 TTTGTGAAATTACCAAAATACCCCTAA
1 TTTGTAAAATTACCAAAATACCCCTAG
* ** *
55533215 TTTGTGAAATTACTGAAATA-CCCTTG
1 TTTGTAAAATTACCAAAATACCCCTAG
* *
55533241 ACTTGTAAAATTACCAAAATACCCCTAA
1 -TTTGTAAAATTACCAAAATACCCCTAG
* *** *
55533269 TTTGTGAAATTATTGAAATA-CCCTTG
1 TTTGTAAAATTACCAAAATACCCCTAG
* * *
55533295 ACTTGTAAAATTACCAAAATACCCTTGG
1 -TTTGTAAAATTACCAAAATACCCCTAG
** *
55533323 TTTACAAAATTACCAAAATACCCCTGG
1 TTTGTAAAATTACCAAAATACCCCTAG
* * *
55533350 TTTGTAAAATTGCCGAAATA-ACCTCAG
1 TTTGTAAAATTACCAAAATACCCCT-AG
* ** *
55533377 TTTGCAAAATTACTGAAATA-CCCTCAA
1 TTTGTAAAATTACCAAAATACCCCT-AG
*
55533404 TTTGTAAAATTACTAAAATACC
1 TTTGTAAAATTACCAAAATACC
55533426 ATCAACTTGT
Statistics
Matches: 237, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
26 11 0.05
27 217 0.92
28 9 0.04
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACCCCTAG
Found at i:55533219 original size:81 final size:81
Alignment explanation
Indices: 55533107--55533425 Score: 325
Period size: 81 Copynumber: 3.9 Consensus size: 81
55533097 ATGCCCTCAA
* * * *
55533107 TTTGTAAAATTACTAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTATAAAATT
1 TTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATT
55533172 ACCAAAATACCCCTAG
66 ACCAAAATACCCCTAG
* * ** ** *
55533188 TTTGTGAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCCTTGACTTGTAAAATT
1 TTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATT
*
55533253 ACCAAAATACCCCTAA
66 ACCAAAATACCCCTAG
* *** * * * *
55533269 TTTGTGAAATTATTGAAATACCCTTGACTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATT
1 TTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATT
*
55533334 ACCAAAATACCCCTGG
66 ACCAAAATACCCCTAG
* * * * * ** *** *
55533350 TTTGTAAAATTGCCGAAATA-ACCTCAGTTTGCAAAATTACTGAAATACCCTCAATTTGTAAAAT
1 TTTGTAAAATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCTTGGTTTATAAAAT
*
55533414 TACTAAAATACC
65 TACCAAAATACC
55533426 ATCAACTTGT
Statistics
Matches: 192, Mismatches: 45, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
80 2 0.01
81 190 0.99
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (81 bp):
TTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATT
ACCAAAATACCCCTAG
Found at i:55533533 original size:27 final size:27
Alignment explanation
Indices: 55533501--55533660 Score: 203
Period size: 27 Copynumber: 5.9 Consensus size: 27
55533491 AAAAATATTG
*
55533501 AATACCCTTGTAGGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
**
55533528 AATACCCCTGTAGGGTAGAATTATTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
55533555 AATACCCCTGTAGGGTAGAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* * **
55533582 AATACCCTTGTAGTGTAGAATTATTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
55533609 AATACCCCTATAGGATAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* * *
55533636 GATACCCTTGTAGGGTAAAATTACC
1 AATACCCCTGTAGGGTAGAATTACC
55533661 ATTTTGCCCC
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAGAATTACCGA
Found at i:55533576 original size:54 final size:54
Alignment explanation
Indices: 55533496--55533658 Score: 247
Period size: 54 Copynumber: 3.0 Consensus size: 54
55533486 TTTACAAAAA
* *
55533496 TATTG-AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAT
1 TATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAT
* *
55533549 TATTGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGTGTAGAAT
1 TATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAT
* * * *
55533603 TATTGAAATACCCCTATAGGATAGAATTACCGAGATACCCTTGTAGGGTAAAAT
1 TATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAT
55533657 TA
1 TA
55533659 CCATTTTGCC
Statistics
Matches: 99, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 5 0.05
54 94 0.95
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (54 bp):
TATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAT
Found at i:55533601 original size:81 final size:81
Alignment explanation
Indices: 55533501--55533659 Score: 228
Period size: 81 Copynumber: 2.0 Consensus size: 81
55533491 AAAAATATTG
* * **
55533501 AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGT
1 AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACCGAAATACCCCTGT
*
55533566 AGGGTAGAATTACTGA
66 AGGGTAAAATTACTGA
* ** * *
55533582 AATACCCTTGTAGTGTAGAATTATTGAAATACCCCTATAGGATAGAATTACCGAGATACCCTTGT
1 AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACCGAAATACCCCTGT
55533647 AGGGTAAAATTAC
66 AGGGTAAAATTAC
55533660 CATTTTGCCC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (81 bp):
AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTACCGAAATACCCCTGT
AGGGTAAAATTACTGA
Found at i:55533939 original size:24 final size:25
Alignment explanation
Indices: 55533863--55533932 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
55533853 AGGAAGTGCT
* * * *
55533863 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGTCCCAGTTTATCA
55533888 AAAAGGGCTTTGTCCCAGTTTATCA
1 AAAAGGGCTTTGTCCCAGTTTATCA
55533913 AAAAGGGCTTTG-CCCGAGTT
1 AAAAGGGCTTTGTCCC-AGTT
55533933 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 3 0.08
25 37 0.93
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGTCCCAGTTTATCA
Found at i:55533945 original size:24 final size:25
Alignment explanation
Indices: 55533863--55533945 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
55533853 AGGAAGTGCT
* * *
55533863 AAAAG-GGCTATGCCCCAGTTTACC
1 AAAAGAGGCTTTGTCCCAGTTTATC
55533887 GAAAAG-GGCTTTGTCCCAGTTTATC
1 -AAAAGAGGCTTTGTCCCAGTTTATC
*
55533912 AAAA-AGGGCTTTG-CCCGAG-TTATT
1 AAAAGA-GGCTTTGTCCC-AGTTTATC
55533936 AAAAGAGGCT
1 AAAAGAGGCT
55533946 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
24 19 0.38
25 31 0.62
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AAAAGAGGCTTTGTCCCAGTTTATC
Found at i:55536866 original size:51 final size:49
Alignment explanation
Indices: 55536699--55536883 Score: 226
Period size: 50 Copynumber: 3.7 Consensus size: 49
55536689 TATCTAGTCG
* *
55536699 CATAGTAGCCTGAACTTAGTACTACACATGCGACCAATTATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACA
* ** * *
55536748 CATAGTAGCCTACACTTAGTACTACACATGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCCGGTACA
** * * * *
55536798 TGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACA
55536849 CATAGTAGCCTGCACTTAGTACTACACATGTGACC
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACC
55536884 TCACAATAGA
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 32 0.29
50 42 0.38
51 38 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACA
Found at i:55536874 original size:101 final size:99
Alignment explanation
Indices: 55536701--55536884 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 99
55536691 TCTAGTCGCA
*
55536701 TAGTAGCCTGAACTTAGTACTACACATGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
1 TAGTAGCCTGAACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
55536766 GTACTACACATGTGACCTAACCATCTGATACATG
66 GTACTACACATGTGACCTAACCATCTGATACATG
* * * * * *
55536800 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGAACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTACACT
55536865 TAGTACTACACATGTGACCT
64 TAGTACTACACATGTGACCT
55536885 CACAATAGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
99 28 0.37
100 3 0.04
101 45 0.59
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGAACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
GTACTACACATGTGACCTAACCATCTGATACATG
Found at i:55537150 original size:26 final size:26
Alignment explanation
Indices: 55537111--55537162 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
55537101 GGTACAACCC
* *
55537111 ATGTAATAATAATTTAACATTCAATT
1 ATGTAACAACAATTTAACATTCAATT
**
55537137 ATGTAACAACAATTTGCCATTCAATT
1 ATGTAACAACAATTTAACATTCAATT
55537163 TCACATGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (26 bp):
ATGTAACAACAATTTAACATTCAATT
Found at i:55542562 original size:50 final size:49
Alignment explanation
Indices: 55542451--55542626 Score: 183
Period size: 50 Copynumber: 3.5 Consensus size: 49
55542441 CTGGTACGCT
* * * ** *
55542451 TAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGATACACA
**
55542500 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCTGATACACA
* * ** *
55542550 TAGTAGCCTGCACTTAGAACTACACACGTGATCGAAGTTATC-GAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-CCATCTGA-TACACA
*
55542601 TAGTAGCCTGCAATTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
55542627 TGCGACCTCA
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 30 0.28
50 45 0.42
51 31 0.29
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGATACACA
Found at i:55542634 original size:101 final size:99
Alignment explanation
Indices: 55542451--55542634 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 99
55542441 CTGGTACGCT
* * * *
55542451 TAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACATAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGAACTACACACGCGACCAATTATCTGGTACACATAGTAGCCTGCAATTA
*
55542516 GTACTACACACGTGACCTAACCATCTGATACATG
66 GTACTACACACGCGACCTAACCATCTGATACATG
* * *
55542550 TAGTAGCCTGCACTTAGAACTACACACGTGATCGAAGTTATC-GAGTACGCATAGTAGCCTGCAA
1 TAGTAGCCTGCACTTAGAACTACACACGCGA-CCAA-TTATCTG-GTACACATAGTAGCCTGCAA
*
55542614 TTAGTACTACACATGCGACCT
63 TTAGTACTACACACGCGACCT
55542635 CACAATAGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 27 0.37
100 4 0.05
101 42 0.58
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGAACTACACACGCGACCAATTATCTGGTACACATAGTAGCCTGCAATTA
GTACTACACACGCGACCTAACCATCTGATACATG
Found at i:55542793 original size:81 final size:81
Alignment explanation
Indices: 55542658--55542820 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
55542648 TCGTATCGTT
*
55542658 TCTATTCCGAAGGCTCAACCGGGAAATTCCTCACTTTCCAACATGTTACAAATTTATTCATAGTC
1 TCTATTCCGAAGACTCAACCGGGAAATTCCTCACTTTCCAACATGTTACAAATTTATTCATAGTC
55542723 CTTTTTCAATTTGCAA
66 CTTTTTCAATTTGCAA
* * *
55542739 TCTATTCTGAAGACTCAACTGGGAAATTCCTCACTTTCGAACATGTTACAAATTTATTCATAGTC
1 TCTATTCCGAAGACTCAACCGGGAAATTCCTCACTTTCCAACATGTTACAAATTTATTCATAGTC
55542804 CTTTTTCAATTTGCAA
66 CTTTTTCAATTTGCAA
55542820 T
1 T
55542821 TTACAACAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTATTCCGAAGACTCAACCGGGAAATTCCTCACTTTCCAACATGTTACAAATTTATTCATAGTC
CTTTTTCAATTTGCAA
Found at i:55542971 original size:27 final size:27
Alignment explanation
Indices: 55542941--55542994 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
55542931 AGGTACAACC
* *
55542941 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
55542968 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
55542995 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:55545819 original size:34 final size:35
Alignment explanation
Indices: 55545775--55545856 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
55545765 TTAGCCCCTT
* **
55545775 TTTCAATAACAGTAT-CAGTTTGGGCCTGAGCCCA
1 TTTCAGTAACAGTATGCAGCCTGGGCCTGAGCCCA
* *
55545809 TTTCAGTAACAG-ATGCAGCCTGGGCCTTATCCCA
1 TTTCAGTAACAGTATGCAGCCTGGGCCTGAGCCCA
*
55545843 TCTCAGT-ACAGTAT
1 TTTCAGTAACAGTAT
55545857 ACAAACAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 6 0.15
34 34 0.85
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
TTTCAGTAACAGTATGCAGCCTGGGCCTGAGCCCA
Found at i:55551708 original size:27 final size:27
Alignment explanation
Indices: 55551678--55551801 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 27
55551668 TGTAGGGTAG
* **
55551678 AATTACTAAAATACCCTTGGTTTAAAA
1 AATTACCAAAATACCCTTGGTTTGTAA
55551705 AATTACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
*
55551732 AATTACCAAAATACACC-TAGTTTGTAA
1 AATTACCAAAATAC-CCTTGGTTTGTAA
* * **
55551759 AATTACTAAAATACCCTCGACTTGTAA
1 AATTACCAAAATACCCTTGGTTTGTAA
* *
55551786 AATTACCGAAGTACCC
1 AATTACCAAAATACCC
55551802 CTAATTTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.02
27 79 0.95
28 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTGTAA
Found at i:55551817 original size:54 final size:54
Alignment explanation
Indices: 55551698--55551817 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
55551688 ATACCCTTGG
* * ** *
55551698 TTTAAAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACACCTAG
1 TTTATAAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACACCTAA
* * * * *
55551752 TTTGTAAAATTACTAAAATACCCTCGACTTGTAAAATTACCGAAGTACCCCTAA
1 TTTATAAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACACCTAA
*
55551806 TTTATAGAATTA
1 TTTATAAAATTA
55551818 TCGTTTTACC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (54 bp):
TTTATAAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACACCTAA
Found at i:55551877 original size:27 final size:27
Alignment explanation
Indices: 55551842--55551926 Score: 118
Period size: 27 Copynumber: 3.1 Consensus size: 27
55551832 ATTTACAAAG
55551842 TTACTGAAATACCCTTGTAGGGTAGAA
1 TTACTGAAATACCCTTGTAGGGTAGAA
* *
55551869 TTA-TCGAAATACCCCTGTAGGTTAGAA
1 TTACT-GAAATACCCTTGTAGGGTAGAA
* *
55551896 TTACTGAGATACCCTTGTAGGGTAAAA
1 TTACTGAAATACCCTTGTAGGGTAGAA
55551923 TTAC
1 TTAC
55551927 CATTTTGCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
TTACTGAAATACCCTTGTAGGGTAGAA
Found at i:55552570 original size:27 final size:27
Alignment explanation
Indices: 55552540--55552641 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
55552530 TCTATTAAGC
* *
55552540 GGCTTTGCCACATTATCTGTTTCTGGT
1 GGCTCTGCCACAATATCTGTTTCTGGT
* *
55552567 GGCTATGCCACAAATATCT-ATTCTGGT
1 GGCTCTGCCAC-AATATCTGTTTCTGGT
* * *
55552594 GGCTCTGCCACAATAACTATATCTGGT
1 GGCTCTGCCACAATATCTGTTTCTGGT
* *
55552621 GACTCTGTCACAATATCTGTT
1 GGCTCTGCCACAATATCTGTT
55552642 CTGTCAGCCA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
26 6 0.10
27 49 0.80
28 6 0.10
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (27 bp):
GGCTCTGCCACAATATCTGTTTCTGGT
Found at i:55552772 original size:6 final size:6
Alignment explanation
Indices: 55552763--55552910 Score: 108
Period size: 6 Copynumber: 24.0 Consensus size: 6
55552753 TTGCATTCAC
* * *
55552763 ATTCTG ATTCTG ATTCT- ATTACCTA ATACTA ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
55552812 ATTCTG -TTACTTG ATAT-TG ATTCTG ATTCTA ATTCTG ATTTTG -TTACCTG
1 ATTCTG ATT-C-TG AT-TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * *
55552862 ATACTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
55552911 TCACTTGATT
Statistics
Matches: 115, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
5 9 0.08
6 92 0.80
7 8 0.07
8 5 0.04
9 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:55552813 original size:37 final size:37
Alignment explanation
Indices: 55552763--55552879 Score: 171
Period size: 37 Copynumber: 3.2 Consensus size: 37
55552753 TTGCATTCAC
* * *
55552763 ATTCTGATTCTGATTCTATTACCTAATACTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTG
* *
55552800 ATTCTGATTCTGATTCTGTTACTTGATATTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTG
* *
55552837 ATTCTAATTCTGATTTTGTTACCTGATACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTG
55552874 ATTCTG
1 ATTCTG
55552880 TCACCTAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (37 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTG
Found at i:55552862 original size:25 final size:25
Alignment explanation
Indices: 55552834--55552904 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
55552824 GATATTGATT
* * *
55552834 CTGATTCTAATTCTGATTTTGTTAC
1 CTGATTCTGATTCTGATTCTGTCAC
*
55552859 CTGATACTGATTCTGATTCTGTCAC
1 CTGATTCTGATTCTGATTCTGTCAC
*
55552884 CTAATTCTGATTCTGATTCTG
1 CTGATTCTGATTCTGATTCTG
55552905 ATTCTGTCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGATTCTGTCAC
Found at i:55552919 original size:25 final size:25
Alignment explanation
Indices: 55552835--55552934 Score: 83
Period size: 25 Copynumber: 3.8 Consensus size: 25
55552825 ATATTGATTC
* * *
55552835 TGATTCTAATTCTGATTTTGTTACC
1 TGATTCTAATTCTGATTCTGTCACT
* *
55552860 TGATACTGATTCTGATTCTGTCACCTAATT
1 TGATTCTAATTCTGATTCTGTCA-C----T
*
55552890 CTGATTCTGATTCTGATTCTGTCACT
1 -TGATTCTAATTCTGATTCTGTCACT
*
55552916 TGATTCTAATTCTAATTCT
1 TGATTCTAATTCTGATTCT
55552935 CATTTTTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
25 36 0.59
26 2 0.03
30 1 0.02
31 22 0.36
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (25 bp):
TGATTCTAATTCTGATTCTGTCACT
Found at i:55552922 original size:31 final size:31
Alignment explanation
Indices: 55552794--55552934 Score: 146
Period size: 31 Copynumber: 4.5 Consensus size: 31
55552784 CCTAATACTA
*
55552794 ATTCTGATTCTGATTCTGATTCTGTTACTTG
1 ATTCTGATTCTGATTCTGATTCTGTCACTTG
* *
55552825 ATAT-TGATTCTGATTCTAATTCTG--ATTTTG
1 AT-TCTGATTCTGATTCTGATTCTGTCA-CTTG
* * *
55552855 -TTACCTGATACTGATTCTGATTCTGTCACCTA
1 ATT--CTGATTCTGATTCTGATTCTGTCACTTG
55552887 ATTCTGATTCTGATTCTGATTCTGTCACTTG
1 ATTCTGATTCTGATTCTGATTCTGTCACTTG
* *
55552918 ATTCTAATTCTAATTCT
1 ATTCTGATTCTGATTCT
55552935 CATTTTTATT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.01
29 2 0.02
30 3 0.03
31 79 0.88
32 2 0.02
33 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGATTCTGTCACTTG
Found at i:55554887 original size:27 final size:27
Alignment explanation
Indices: 55554857--55554952 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 27
55554847 TGTAGGGTAG
*
55554857 AATTACTAAAATACCATTGGTTTAAAA
1 AATTACCAAAATACCATTGGTTTAAAA
* **
55554884 AATTACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCATTGGTTTAAAA
* * **
55554911 AATTACCAAAATA-CACCTAGTTTGTAA
1 AATTACCAAAATACCA-TTGGTTTAAAA
55554938 AATTACCAAAATACC
1 AATTACCAAAATACC
55554953 CTCAATTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 58 0.97
28 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCATTGGTTTAAAA
Found at i:55554961 original size:27 final size:27
Alignment explanation
Indices: 55554882--55555034 Score: 155
Period size: 27 Copynumber: 5.7 Consensus size: 27
55554872 ATTGGTTTAA
* *
55554882 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*
55554909 AAAATTACCAAAATACACCTAG-TTTGT
1 AAAATTACCAAAATAC-CCTCGATTTGT
*
55554936 AAAATTACCAAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * * * * **
55554963 GAATTTACTAAAATATCCTTGACCTGT
1 AAAATTACCAAAATACCCTCGATTTGT
** *
55554990 AAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*
55555017 AAAATTACCAAAGTACCC
1 AAAATTACCAAAATACCC
55555035 CTAATTTATA
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.03
27 97 0.93
28 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:55555110 original size:27 final size:27
Alignment explanation
Indices: 55555075--55555159 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
55555065 ATTTACAAAG
*
55555075 TTACTGAAATACCCTTATAGGGTAGAA
1 TTACTGAAATACCCTTGTAGGGTAGAA
* *
55555102 TTA-TCGAAATACCCCTGTAGGTTAGAA
1 TTACT-GAAATACCCTTGTAGGGTAGAA
* * *
55555129 TTACTGAGATACCCTTGTGGGGTAAAA
1 TTACTGAAATACCCTTGTAGGGTAGAA
55555156 TTAC
1 TTAC
55555160 CATTTTGCCC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.96
28 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
TTACTGAAATACCCTTGTAGGGTAGAA
Found at i:55555170 original size:27 final size:27
Alignment explanation
Indices: 55555140--55555203 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
55555130 TACTGAGATA
*
55555140 CCCTTGTGGGGTAAAATTACCATTTTG
1 CCCTTGTGGGGTAAAATAACCATTTTG
* * *
55555167 CCCTTAG-GGTGTTAAATAACTATTTTG
1 CCCTT-GTGGGGTAAAATAACCATTTTG
*
55555194 CCATTGTGGG
1 CCCTTGTGGG
55555204 CAAGTGACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 27 0.93
28 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (27 bp):
CCCTTGTGGGGTAAAATAACCATTTTG
Found at i:55555600 original size:22 final size:22
Alignment explanation
Indices: 55555548--55555612 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
55555538 GCCAATTATT
* *
55555548 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
55555570 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
55555592 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
55555613 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:55555801 original size:27 final size:27
Alignment explanation
Indices: 55555771--55555878 Score: 130
Period size: 27 Copynumber: 4.0 Consensus size: 27
55555761 ATTCTGTTAA
* *
55555771 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
55555798 GTGGCTATGCCACAAATATCT-ATTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
55555825 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
55555852 GTGACTCTGTCACAATATCTG-TTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
55555878 G
1 G
55555879 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 12 0.17
27 52 0.74
28 6 0.09
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:55555829 original size:54 final size:53
Alignment explanation
Indices: 55555771--55555878 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 53
55555761 ATTCTGTTAA
* * * *
55555771 GTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTATTCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCAC-AATATCTATTCTG
* * *
55555825 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTATTCTG
55555878 G
1 G
55555879 CAGCCATGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 13 0.28
54 34 0.72
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTATTCTG
Done.