Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007757.1 Hibiscus syriacus cultivar Beakdansim tig00110023_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 203134
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5818 original size:246 final size:245
Alignment explanation
Indices: 5371--5874 Score: 951
Period size: 247 Copynumber: 2.1 Consensus size: 245
5361 TATTCTATCA
5371 TAACCATGCATTCACATGTTAGTATAAATTATATCTTATTATTTCTATCCTATGCTTATTTGATC
1 TAACCATGCATTCACATGTTAGTATAAATTATATCTTATTATTTCTATCCTATGCTTATTTGATC
5436 ATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTCTTAGGATATTATTATTACA
66 ATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTCTTAGGATATTATTATTACA
5501 TGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATATCC
131 TGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATATCC
5566 ACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
196 ACAATATTATTTCAAGTA-GTTAAGTATGTTATATTAGTCTTGCATTCATT
5617 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
1 TAACCATGCATTCACATGTTAGTATAAATTA-TATCTTATTATTTCTATCCTATGCTTATTTGAT
5682 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
65 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCA-TTCTTAGGATATTATTATTA
5747 C-TGTTTCCATTTATCATTTATTATGAATA-CATGTTAAATGATATTCATGCATACAACATATAT
129 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
5810 CCACAATATTATTTCAAGTAGTTAAGTATGTTATATTAGTCTTGCATTCATT
194 CCACAATATTATTTCAAGTAGTTAAGTATGTTATATTAGTCTTGCATTCATT
*
5862 TAAGCATG-ATTCA
1 TAACCATGCATTCA
5875 ATTCATTCGT
Statistics
Matches: 255, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
244 5 0.02
245 39 0.15
246 85 0.33
247 105 0.41
248 21 0.08
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (245 bp):
TAACCATGCATTCACATGTTAGTATAAATTATATCTTATTATTTCTATCCTATGCTTATTTGATC
ATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTCTTAGGATATTATTATTACA
TGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATATCC
ACAATATTATTTCAAGTAGTTAAGTATGTTATATTAGTCTTGCATTCATT
Found at i:8251 original size:16 final size:16
Alignment explanation
Indices: 8230--8261 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8220 TAGTTAGCTC
8230 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
8246 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
8262 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:9699 original size:11 final size:11
Alignment explanation
Indices: 9674--9766 Score: 84
Period size: 11 Copynumber: 8.5 Consensus size: 11
9664 GTGCAAAAAT
9674 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
9687 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
9698 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
9709 GAAGAAAAGAA
1 AAAGAAAAGAA
*
9720 GAAGAAAAG-A
1 AAAGAAAAGAA
9730 AAAGAAAAGAA
1 AAAGAAAAGAA
*
9741 GAAGAAAAG-A
1 AAAGAAAAGAA
9751 AAAGAAAAGAA
1 AAAGAAAAGAA
9762 AAAGA
1 AAAGA
9767 GAAGTTCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
10 21 0.32
11 35 0.53
12 2 0.03
13 8 0.12
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:9708 original size:19 final size:19
Alignment explanation
Indices: 9686--9770 Score: 77
Period size: 19 Copynumber: 4.4 Consensus size: 19
9676 AGAAAAGACA
**
9686 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAAGAAG
9705 AAAAGAAGA-AAAGAAGAAG
1 AAAAGAAGAGAAA-AAGAAG
*
9724 AAAAGAAAAGAAAAGAAGAAG
1 AAAAGAAGAG-AAA-AAGAAG
*
9745 AAAAGAAAAG-AAAAGAA-
1 AAAAGAAGAGAAAAAGAAG
9762 AAAGAGAAG
1 AAA-AGAAG
9771 TTCAAAAAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
17 3 0.05
18 12 0.21
19 23 0.40
21 20 0.34
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (19 bp):
AAAAGAAGAGAAAAAGAAG
Found at i:9711 original size:5 final size:5
Alignment explanation
Indices: 9674--9763 Score: 91
Period size: 5 Copynumber: 18.6 Consensus size: 5
9664 GTGCAAAAAT
* * **
9674 AAAGA AAAG- ACA-A AAAGA AGAGA AAA-A TCAGA AAAG- -AAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
9719 AGAAGA AAAGA AAAGA AAAGA AGAAGA AAAGA AAAGA AAAGA AAA
1 A-AAGA AAAGA AAAGA AAAGA A-AAGA AAAGA AAAGA AAAGA AAA
9764 AGAGAAGTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
3 3 0.04
4 6 0.09
5 51 0.73
6 10 0.14
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:9736 original size:21 final size:21
Alignment explanation
Indices: 9703--9766 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
9693 GAGAAAAATC
9703 AGAAAAG--AAGAAAAGAAGA
1 AGAAAAGAAAAGAAAAGAAGA
9722 AGAAAAGAAAAGAAAAGAAGA
1 AGAAAAGAAAAGAAAAGAAGA
*
9743 AGAAAAGAAAAGAAAAGAAAA
1 AGAAAAGAAAAGAAAAGAAGA
9764 AGA
1 AGA
9767 GAAGTTCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 7 0.17
21 35 0.83
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AGAAAAGAAAAGAAAAGAAGA
Found at i:9766 original size:16 final size:15
Alignment explanation
Indices: 9674--9763 Score: 91
Period size: 16 Copynumber: 6.2 Consensus size: 15
9664 GTGCAAAAAT
*
9674 AAAGAAAAG-ACA-A
1 AAAGAAAAGAAAAGA
*
9687 AAAGAAGAGAAAA-A
1 AAAGAAAAGAAAAGA
**
9701 TCAGAAAAG--AAGA
1 AAAGAAAAGAAAAGA
9714 AAAGAAGAAGAAAAGA
1 AAAGAA-AAGAAAAGA
9730 AAAGAAAAGAAGAAGA
1 AAAGAAAAGAA-AAGA
9746 AAAGAAAAGAAAAGA
1 AAAGAAAAGAAAAGA
9761 AAA
1 AAA
9764 AGAGAAGTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.03
13 13 0.20
14 12 0.19
15 12 0.19
16 25 0.39
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (15 bp):
AAAGAAAAGAAAAGA
Found at i:11883 original size:16 final size:16
Alignment explanation
Indices: 11862--11893 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11852 TAGTTAGCTC
11862 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
11878 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
11894 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:13324 original size:18 final size:18
Alignment explanation
Indices: 13303--13337 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13293 TTACACACTT
13303 TGCCACAACAACACCATC
1 TGCCACAACAACACCATC
*
13321 TGCCACGACAACACCAT
1 TGCCACAACAACACCAT
13338 TCATACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11
Consensus pattern (18 bp):
TGCCACAACAACACCATC
Found at i:22105 original size:19 final size:19
Alignment explanation
Indices: 22081--22117 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22071 CGGCCAAGAG
22081 CATGTATATGCATTAAAAT
1 CATGTATATGCATTAAAAT
* *
22100 CATGTATTTTCATTAAAA
1 CATGTATATGCATTAAAA
22118 AAATCATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (19 bp):
CATGTATATGCATTAAAAT
Found at i:22591 original size:21 final size:21
Alignment explanation
Indices: 22552--22595 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
22542 GCCATCTCTA
22552 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
22574 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
22595 T
1 T
22596 AATTTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:26897 original size:22 final size:22
Alignment explanation
Indices: 26872--26913 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
26862 CTATTCATTT
26872 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
26894 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
26914 CCAGCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:27286 original size:12 final size:12
Alignment explanation
Indices: 27271--27295 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27261 AAAGAGAGGC
27271 AAAAAACAAAAA
1 AAAAAACAAAAA
27283 AAAAAACAAAAA
1 AAAAAACAAAAA
27295 A
1 A
27296 GCTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:31550 original size:22 final size:22
Alignment explanation
Indices: 31525--31566 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31515 CAATTCATTT
*
31525 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTCGTTTTA
31547 ATCTTATTTTTATCTCGTTT
1 ATCTTATTTTTATCTCGTTT
31567 CCAGCACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (22 bp):
ATCTTATTTTTATCTCGTTTTA
Found at i:70732 original size:20 final size:21
Alignment explanation
Indices: 70709--70762 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
70699 TTTTTTGAAA
*
70709 TTTTGGCTTTTTTGGC-TCTT
1 TTTTGGCTTTTTTGCCTTCTT
* * *
70729 TTTTTGTTTTTTTGCCTTTTT
1 TTTTGGCTTTTTTGCCTTCTT
*
70750 TTTTGCCTTTTTT
1 TTTTGGCTTTTTT
70763 TTGTTTTTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (21 bp):
TTTTGGCTTTTTTGCCTTCTT
Found at i:70738 original size:19 final size:18
Alignment explanation
Indices: 70716--70751 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
70706 AAATTTTGGC
70716 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
70735 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
70752 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:70765 original size:11 final size:12
Alignment explanation
Indices: 70735--70764 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
70725 TCTTTTTTTG
70735 TTTTTTTGCCTT
1 TTTTTTTGCCTT
70747 TTTTTTTGCCTT
1 TTTTTTTGCCTT
70759 TTTTTT
1 TTTTTT
70765 GTTTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:78174 original size:19 final size:20
Alignment explanation
Indices: 78136--78174 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
78126 ATCATTCACT
*
78136 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
78156 TGCATAATATATG-TTTTCA
1 TGCATAATATATGATTTTCA
78175 CATCTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:79186 original size:19 final size:20
Alignment explanation
Indices: 79162--79212 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
79152 CGGCCAAGAG
* *
79162 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
79181 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
79201 CATGTATTTTCA
1 CATGTATTTTCA
79213 AAGGGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:81482 original size:36 final size:36
Alignment explanation
Indices: 81378--81474 Score: 194
Period size: 36 Copynumber: 2.7 Consensus size: 36
81368 AAATGGAATT
81378 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
81414 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
81450 TGGTGATGATATAGGCGTGATAATG
1 TGGTGATGATATAGGCGTGATAATG
81475 ATTATGGACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:83177 original size:15 final size:14
Alignment explanation
Indices: 83159--83199 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
83149 TTAAAAAAAA
83159 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
83174 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
83188 AAAAAAACAAAA
1 AAAAAAA-AAAA
83200 AAAAGAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:83180 original size:22 final size:21
Alignment explanation
Indices: 83152--83221 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
83142 TATTTTTTTA
83152 AAAAAAAAAAACAAAAAAAGGC
1 AAAAAAAAAAACAAAAAAA-GC
83174 AAAAAAAAAAAGGCAAAAAAA-C
1 AAAAAAAAAAA--CAAAAAAAGC
* * *
83196 AAAAAAAAGAGCCAAAAAAGC
1 AAAAAAAAAAACAAAAAAAGC
*
83217 CAAAA
1 AAAAA
83222 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 21 0.51
24 8 0.20
ACGTcount: A:0.79, C:0.11, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAAGC
Found at i:83183 original size:24 final size:22
Alignment explanation
Indices: 83151--83203 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
83141 CTATTTTTTT
83151 AAAAAAAAAAAACAAAAAAAGGCA
1 AAAAAAAAAAAACAAAAAAA--CA
**
83175 AAAAAAAAAAGGCAAAAAAACA
1 AAAAAAAAAAAACAAAAAAACA
83197 AAAAAAA
1 AAAAAAA
83204 GAGCCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 9 0.33
24 18 0.67
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAACAAAAAAACA
Found at i:83199 original size:20 final size:21
Alignment explanation
Indices: 83175--83214 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83165 AAAAAAGGCA
* *
83175 AAAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAGAGCCAAAAAAAC
83196 AAAAAAAAGAGCCAAAAAA
1 AAAAAAAAGAGCCAAAAAA
83215 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAGCCAAAAAAAC
Found at i:83221 original size:21 final size:21
Alignment explanation
Indices: 83151--83214 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 21
83141 CTATTTTTTT
**
83151 AAAAAAAAAAAACAAAAAAAGGC
1 AAAAAAAAAAGCCAAAAAAA--C
*
83174 AAAAAAAAAAAGGCAAAAAAAC
1 -AAAAAAAAAAGCCAAAAAAAC
*
83196 AAAAAAAAGAGCCAAAAAA
1 AAAAAAAAAAGCCAAAAAA
83215 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 17 0.47
22 1 0.03
24 18 0.50
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGCCAAAAAAAC
Found at i:100018 original size:6 final size:6
Alignment explanation
Indices: 100007--100049 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
99997 GATGTAGGAG
*
100007 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
100050 TTGTTGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:100037 original size:20 final size:19
Alignment explanation
Indices: 100007--100049 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
99997 GATGTAGGAG
100007 TCTTTTTC-T-TTTCTTTT
1 TCTTTTTCTTCTTTCTTTT
*
100024 TGTTTTTCTTCTTTCTTTT
1 TCTTTTTCTTCTTTCTTTT
100043 TCTTTTT
1 TCTTTTT
100050 TTGTTGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (19 bp):
TCTTTTTCTTCTTTCTTTT
Found at i:100888 original size:19 final size:20
Alignment explanation
Indices: 100841--100891 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
100831 GAAACGCCTT
**
100841 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
100861 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
100880 TGAAGATACATG
1 TGAAAATACATG
100892 CTCTTGGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:105830 original size:8 final size:8
Alignment explanation
Indices: 105817--105879 Score: 76
Period size: 8 Copynumber: 8.0 Consensus size: 8
105807 ATTTTTTTTT
105817 CAAAAAAA
1 CAAAAAAA
105825 CAAAAAAA
1 CAAAAAAA
105833 C-AAAAAA
1 CAAAAAAA
*
105840 CAAAAAAGG
1 CAAAAAA-A
105849 CAAAAAAA
1 CAAAAAAA
**
105857 -AAAAAGG
1 CAAAAAAA
105864 CAAAAAAA
1 CAAAAAAA
105872 CAAAAAAA
1 CAAAAAAA
105880 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 12 0.26
8 27 0.59
9 7 0.15
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:105837 original size:6 final size:7
Alignment explanation
Indices: 105819--105878 Score: 59
Period size: 7 Copynumber: 7.9 Consensus size: 7
105809 TTTTTTTTCA
105819 AAAAAAC
1 AAAAAAC
105826 AAAAAAAC
1 -AAAAAAC
105834 AAAAAAC
1 AAAAAAC
105841 AAAAAAGGC
1 AAAAAA--C
105850 AAAAAA-
1 AAAAAAC
105856 AAAAAAGGC
1 AAAAAA--C
105865 AAAAAAAC
1 -AAAAAAC
105873 AAAAAA
1 AAAAAA
105879 AGAGCCAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.13
7 19 0.41
8 8 0.17
9 7 0.15
10 6 0.13
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:105839 original size:15 final size:16
Alignment explanation
Indices: 105819--105878 Score: 79
Period size: 15 Copynumber: 3.8 Consensus size: 16
105809 TTTTTTTTCA
105819 AAAAAACAAAAAA-AC
1 AAAAAACAAAAAAGAC
*
105834 AAAAAACAAAAAAGGC
1 AAAAAACAAAAAAGAC
*
105850 AAAAAA-AAAAAAGGC
1 AAAAAACAAAAAAGAC
105865 AAAAAAACAAAAAA
1 -AAAAAACAAAAAA
105879 AGAGCCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
15 22 0.54
16 13 0.32
17 6 0.15
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAGAC
Found at i:105870 original size:32 final size:32
Alignment explanation
Indices: 105817--105878 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
105807 ATTTTTTTTT
105817 CAAAAAAACAAAAAAACAAAAAACAAAAAAGG
1 CAAAAAAACAAAAAAACAAAAAACAAAAAAGG
**
105849 CAAAAAAA-AAAAAGGCAAAAAAACAAAAAA
1 CAAAAAAACAAAAAAAC-AAAAAACAAAAAA
105879 AGAGCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.00
Consensus pattern (32 bp):
CAAAAAAACAAAAAAACAAAAAACAAAAAAGG
Found at i:105897 original size:20 final size:20
Alignment explanation
Indices: 105853--105890 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
105843 AAAAGGCAAA
*
105853 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
105873 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
105891 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:110994 original size:19 final size:20
Alignment explanation
Indices: 110947--110997 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
110937 AAAACGCCTT
**
110947 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
110967 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
110986 TGAAGATACATG
1 TGAAAATACATG
110998 CTCTTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:115318 original size:15 final size:16
Alignment explanation
Indices: 115297--115354 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
115287 AAGATATGGT
115297 AATGAAATAAGAAA-A
1 AATGAAATAAGAAAGA
* *
115312 GATGAAATAATAAAGA
1 AATGAAATAAGAAAGA
*
115328 AATGAAAT-AGTAAGAA
1 AATGAAATAAGAAAG-A
115344 AATGAAGATAA
1 AATGAA-ATAA
115355 CTTACAACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 16 0.47
16 15 0.44
17 2 0.06
18 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AATGAAATAAGAAAGA
Found at i:115334 original size:16 final size:16
Alignment explanation
Indices: 115297--115354 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
115287 AAGATATGGT
*
115297 AATGAAATAAGAAA-A
1 AATGAAATAATAAAGA
*
115312 GATGAAATAATAAAGA
1 AATGAAATAATAAAGA
*
115328 AATGAAATAGT-AAGAA
1 AATGAAATAATAAAG-A
115344 AATGAAGATAA
1 AATGAA-ATAA
115355 CTTACAACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 15 0.43
16 17 0.49
17 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AATGAAATAATAAAGA
Found at i:116981 original size:11 final size:11
Alignment explanation
Indices: 116965--116994 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
116955 TGTCTCAAAA
*
116965 TGTCCTTGAGT
1 TGTCCTAGAGT
116976 TGTCCTAGAGT
1 TGTCCTAGAGT
116987 TGTCCTAG
1 TGTCCTAG
116995 TCAAGTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (11 bp):
TGTCCTAGAGT
Found at i:119048 original size:29 final size:29
Alignment explanation
Indices: 118984--119041 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
118974 TGCGATGAAA
118984 GATATTTCCTTTCATCTTGTCAATAGTTT
1 GATATTTCCTTTCATCTTGTCAATAGTTT
119013 GATATTTCCTTTCATCTTGTCAATAGTTT
1 GATATTTCCTTTCATCTTGTCAATAGTTT
119042 TTCATTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (29 bp):
GATATTTCCTTTCATCTTGTCAATAGTTT
Found at i:120941 original size:19 final size:19
Alignment explanation
Indices: 120917--120953 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
120907 CGGCCAAGAG
120917 CATGTATATACATTAAAAT
1 CATGTATATACATTAAAAT
* *
120936 CATGTATTTTCATTAAAA
1 CATGTATATACATTAAAA
120954 AAATCATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (19 bp):
CATGTATATACATTAAAAT
Found at i:132758 original size:33 final size:33
Alignment explanation
Indices: 132679--132782 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
132669 ATACAATCTG
* *
132679 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
132715 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
132748 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
132781 TC
1 TC
132783 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:138435 original size:33 final size:33
Alignment explanation
Indices: 138356--138459 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
138346 ATACAATCTG
* *
138356 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
138392 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
138425 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
138458 TC
1 TC
138460 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:138810 original size:36 final size:35
Alignment explanation
Indices: 138756--138831 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
138746 CCTCACATCA
*
138756 ATAGGCGTGCAATGGTGATGGAAGATGGTGATCTT
1 ATAGGCGTGAAATGGTGATGGAAGATGGTGATCTT
*
138791 ATAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT
1 ATAGGCGTG-AAATGGTGATGGAAGATGGTGATCTT
138827 ATAGG
1 ATAGG
138832 TAGTATCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.24
36 29 0.76
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.28
Consensus pattern (35 bp):
ATAGGCGTGAAATGGTGATGGAAGATGGTGATCTT
Found at i:142371 original size:19 final size:19
Alignment explanation
Indices: 142321--142374 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
142311 CTTTCTTCAC
*
142321 TTTTTCTTTCTCTTTGAAT
1 TTTTTCTTTCTTTTTGAAT
* **
142340 TTCTTCTTTTCTTTTTGTTT
1 TTTTTC-TTTCTTTTTGAAT
142360 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
142375 CTCTTTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTGAAT
Found at i:142391 original size:27 final size:27
Alignment explanation
Indices: 142339--142391 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
142329 TCTCTTTGAA
**
142339 TTTCTTCTTTTCTTTTTGTTTTTTTTC
1 TTTCTTCTTTTCTTTTTGTTGATTTTC
142366 TTTCTT-TTTCTCTTTTTGTTGATTTT
1 TTTCTTCTTT-TCTTTTTGTTGATTTT
142392 GTTGCAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (27 bp):
TTTCTTCTTTTCTTTTTGTTGATTTTC
Found at i:142784 original size:33 final size:33
Alignment explanation
Indices: 142742--142810 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
142732 GTTGATGAAT
*
142742 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
142775 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
142808 GAA
1 GAA
142811 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:146524 original size:33 final size:33
Alignment explanation
Indices: 146482--146550 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
146472 GTTGATGAAT
*
146482 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
146515 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
146548 GAA
1 GAA
146551 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:148281 original size:13 final size:13
Alignment explanation
Indices: 148263--148320 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
148253 TAGGCGTGCA
148263 ATGGTGATGAAAG
1 ATGGTGATGAAAG
** *
148276 ATGGTGATGTTAT
1 ATGGTGATGAAAG
*
148289 A-GGCG-TGAAA-
1 ATGGTGATGAAAG
*
148299 ATGGTGATGGAAG
1 ATGGTGATGAAAG
148312 ATGGTGATG
1 ATGGTGATG
148321 TTATATGTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 7 0.21
13 20 0.59
ACGTcount: A:0.31, C:0.02, G:0.40, T:0.28
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:148307 original size:36 final size:35
Alignment explanation
Indices: 148216--148325 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
148206 TTGGTGGTTA
* * **
148216 TATAGGCGTGAAATGGTGAT-AGAAGTTGATGATAA
1 TATAGGCGTGAAATGGTGATGA-AAGATGGTGATGT
*
148251 TATAGGCGTGCAATGGTGATGAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
*
148286 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGAAAGATGGTGATGT
148322 TATA
1 TATA
148326 TGTAGTATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 38 0.58
36 28 0.42
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
Found at i:151115 original size:33 final size:33
Alignment explanation
Indices: 151036--151139 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
151026 ATACAATCTG
* *
151036 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
151072 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
151105 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
151138 TC
1 TC
151140 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:155583 original size:33 final size:33
Alignment explanation
Indices: 155504--155607 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
155494 ATACAATCTG
* *
155504 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
155540 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
155573 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
155606 TC
1 TC
155608 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:165496 original size:15 final size:15
Alignment explanation
Indices: 165478--165507 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
165468 TTTCTTTGAA
165478 TTTTTTTC-TTCTTT
1 TTTTTTTCTTTCTTT
165492 TTTTTTTCTTTCTTT
1 TTTTTTTCTTTCTTT
165507 T
1 T
165508 GCACTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTCTTTCTTT
Found at i:165574 original size:19 final size:19
Alignment explanation
Indices: 165531--165575 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
165521 GTTATAGGAG
* * *
165531 TCTTTTTTTTCTTTTTGTT
1 TCTTTTTCTTCTTTCTATT
*
165550 TATTTTTCTTCTTTCTATT
1 TCTTTTTCTTCTTTCTATT
165569 TCTTTTT
1 TCTTTTT
165576 TGTTGCAGCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (19 bp):
TCTTTTTCTTCTTTCTATT
Found at i:166400 original size:19 final size:20
Alignment explanation
Indices: 166362--166402 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
166352 GAAACCCCTT
*
166362 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
166382 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
166401 TG
1 TG
166403 CAGATAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:169060 original size:13 final size:13
Alignment explanation
Indices: 169038--169067 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
169028 ACTAAACACC
169038 TTTC-ACATACCT
1 TTTCAACATACCT
169050 TTTCAACATACCT
1 TTTCAACATACCT
169063 TTTCA
1 TTTCA
169068 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:174795 original size:18 final size:18
Alignment explanation
Indices: 174772--174806 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
174762 ATATTAATCC
174772 CGTAATATTTACAAAATT
1 CGTAATATTTACAAAATT
174790 CGTAATATTTACAAAAT
1 CGTAATATTTACAAAAT
174807 CCCGTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
CGTAATATTTACAAAATT
Found at i:188809 original size:11 final size:11
Alignment explanation
Indices: 188795--188829 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
188785 TCCGAAAATT
*
188795 AAAAAAATAAA
1 AAAAAAAGAAA
188806 AAAAAAAGAAA
1 AAAAAAAGAAA
*
188817 AGAAAAAGAAA
1 AAAAAAAGAAA
188828 AA
1 AA
188830 GAATTCTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:195760 original size:20 final size:21
Alignment explanation
Indices: 195723--195761 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
195713 GATGGTCTTG
*
195723 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
195744 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
195762 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:198239 original size:14 final size:15
Alignment explanation
Indices: 198220--198248 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
198210 TAGTTCACAT
198220 CATTATA-ATATGCA
1 CATTATATATATGCA
198234 CATTATATATATGCA
1 CATTATATATATGCA
198249 TTATATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (15 bp):
CATTATATATATGCA
Found at i:199097 original size:21 final size:19
Alignment explanation
Indices: 199050--199101 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
199040 CGGCCAAGAG
*
199050 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
199069 CATATATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
199090 CATGTATTTTCA
1 CATGTATTTTCA
199102 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Done.