Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold680
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: 1139231
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.15
Warning! 618122 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:121795 original size:13 final size:13
Alignment explanation
Indices: 121777--121802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
121767 ACACCAAAGT
121777 ATGTATCGATACA
1 ATGTATCGATACA
121790 ATGTATCGATACA
1 ATGTATCGATACA
121803 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:121800 original size:33 final size:34
Alignment explanation
Indices: 121758--121823 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
121748 TAGCCAAACT
* **
121758 TGTATCGATACACCAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
121791 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
121824 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:122937 original size:15 final size:16
Alignment explanation
Indices: 122917--122950 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
122907 TTATATATAC
*
122917 CAAAAT-TAATTAAAT
1 CAAAATATAATAAAAT
122932 CAAAATATAATAAAAT
1 CAAAATATAATAAAAT
122948 CAA
1 CAA
122951 TTAAATGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (16 bp):
CAAAATATAATAAAAT
Found at i:123206 original size:9 final size:9
Alignment explanation
Indices: 123194--123245 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
123184 TTGATTAAAT
123194 TTAATTTAA
1 TTAATTTAA
123203 TTAA-TTAA
1 TTAATTTAA
123211 TTAATTTAA
1 TTAATTTAA
*
123220 TTTATTTTTAA
1 -TTA-ATTTAA
*
123231 TCAATTTAA
1 TTAATTTAA
*
123240 ATAATT
1 TTAATT
123246 GATTTAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.23
9 17 0.49
10 5 0.14
11 5 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATTTAA
Found at i:123212 original size:13 final size:13
Alignment explanation
Indices: 123194--123262 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
123184 TTGATTAAAT
123194 TTAATTTAATTAA
1 TTAATTTAATTAA
123207 TTAA-TTAATTTAA
1 TTAATTTAA-TTAA
*
123220 TTTATTT--TTAA
1 TTAATTTAATTAA
* *
123231 TCAATTTAAATAA
1 TTAATTTAATTAA
* *
123244 TTGATTTAATTGA
1 TTAATTTAATTAA
123257 TTAATT
1 TTAATT
123263 CAGTCAGTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
11 9 0.21
12 4 0.09
13 28 0.65
14 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:123305 original size:22 final size:21
Alignment explanation
Indices: 123279--123332 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
123269 GTTTTTAATT
123279 ATTAAAATATGAAATTAAATAA
1 ATTAAAATATGAAATTAAAT-A
* *
123301 ATTAAAATAATTAAATTTAATA
1 ATTAAAAT-ATGAAATTAAATA
*
123323 TTTAAAATAT
1 ATTAAAATAT
123333 ATTTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 16 0.57
23 10 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTAAAATATGAAATTAAATA
Found at i:125049 original size:2 final size:2
Alignment explanation
Indices: 125042--125070 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
125032 AAATTAACAA
125042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
125071 CTTTTTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125660 original size:18 final size:17
Alignment explanation
Indices: 125622--125663 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
125612 TGTTTAAAGT
*
125622 ATTTTATATTTATATAG
1 ATTTTATATTTATATAA
125639 ATTTTGATATGTTA-ATAA
1 ATTTT-ATAT-TTATATAA
125657 ATTTTAT
1 ATTTTAT
125664 TATATAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:126424 original size:16 final size:16
Alignment explanation
Indices: 126403--126437 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
126393 ATTTGTATTT
*
126403 TAATTAATGATATTAA
1 TAATTAATGATACTAA
*
126419 TAATTAATTATACTAA
1 TAATTAATGATACTAA
126435 TAA
1 TAA
126438 ATATTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATTAATGATACTAA
Found at i:126472 original size:23 final size:23
Alignment explanation
Indices: 126416--126474 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
126406 TTAATGATAT
126416 TAATAATTAATTATACTAATAAA
1 TAATAATTAATTATACTAATAAA
* *
126439 TATTAAGTAATTATACTAATAAA
1 TAATAATTAATTATACTAATAAA
126462 TAA-ATATTAATTA
1 TAATA-ATTAATTA
126475 ATTGAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATAATTAATTATACTAATAAA
Found at i:127153 original size:6 final size:6
Alignment explanation
Indices: 127142--127172 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
127132 TGAAACTTGC
127142 TTATAG TTATAG TTATAG TTATAG ATTATAG
1 TTATAG TTATAG TTATAG TTATAG -TTATAG
127173 ATTTAGAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
TTATAG
Found at i:130338 original size:24 final size:24
Alignment explanation
Indices: 130302--130358 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
130292 GTTGAGAGTT
*
130302 TATTTATATTTTTAAATTAAATCA
1 TATTTATAATTTTAAATTAAATCA
*
130326 TATTTATAATTTTAAATTAAATTA
1 TATTTATAATTTTAAATTAAATCA
130350 TATTATATA
1 TATT-TATA
130359 TACTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTATAATTTTAAATTAAATCA
Found at i:131005 original size:16 final size:16
Alignment explanation
Indices: 130964--131007 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
130954 TTAAAAATAG
130964 TAAATTTTATATTAACA
1 TAAATTTT-TATTAACA
* *
130981 TAAAATTTTATTAATA
1 TAAATTTTTATTAACA
*
130997 TACATTTTTAT
1 TAAATTTTTAT
131008 AATTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTTTTATTAACA
Found at i:131326 original size:2 final size:2
Alignment explanation
Indices: 131321--131345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131311 ACGTACACAC
131321 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
131346 AAATAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:133560 original size:42 final size:42
Alignment explanation
Indices: 133505--133587 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
133495 AGTAAAGTTA
133505 TGTTATTATGAAAACACTCATATATATATATATATATATATG
1 TGTTATTATGAAAACACTCATATATATATATATATATATATG
133547 TGTTATTATGAAAACACTCATATATATATATATATATATAT
1 TGTTATTATGAAAACACTCATATATATATATATATATATAT
133588 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (42 bp):
TGTTATTATGAAAACACTCATATATATATATATATATATATG
Found at i:133573 original size:2 final size:2
Alignment explanation
Indices: 133566--133599 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
133556 GAAAACACTC
133566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133600 GTAGATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133743 original size:12 final size:12
Alignment explanation
Indices: 133708--133742 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
133698 TATTAATTAT
*
133708 TTTATAATAATA
1 TTTATAATAAAA
133720 TTTATAATAAAA
1 TTTATAATAAAA
133732 TTTA-AATAAAA
1 TTTATAATAAAA
133743 AAGTTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTATAATAAAA
Found at i:136427 original size:19 final size:20
Alignment explanation
Indices: 136385--136433 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
136375 TTTAAATTTA
*
136385 ATAAAAATAATATATTAAAT
1 ATAAAAATAATAAATTAAAT
136405 ATAAAAA-AATAAATT-AAT
1 ATAAAAATAATAAATTAAAT
136423 GAT-AAAATAAT
1 -ATAAAAATAAT
136434 CTTTAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAAAATAATAAATTAAAT
Found at i:141524 original size:20 final size:20
Alignment explanation
Indices: 141499--141554 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
141489 TTTACCCAGA
141499 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTTCAT
*
141519 TGTATCGATATATTTTTCAT
1 TGTATCGATACATTTTTCAT
141539 TGTATCGATACATTTT
1 TGTATCGATACATTTT
141555 GGGTTTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAT
Found at i:141527 original size:70 final size:71
Alignment explanation
Indices: 141448--141604 Score: 235
Period size: 70 Copynumber: 2.2 Consensus size: 71
141438 TTTTAATAAT
141448 TTGTATCGATACATTCTTCATTATATCGATACATTCTAGGTTTT-ACCCAGATGTATCGATACAT
1 TTGTATCGATACATTCTTCATTATATCGATACATTCTAGGTTTTAACCCAGATGTATCGATACAT
*
141512 TTTTCA
66 TTCTCA
* * * * * *
141518 TTGTATCGATATATTTTTCATTGTATCGATACATTTTGGGTTTTAACTCAGATGTATCGATACAT
1 TTGTATCGATACATTCTTCATTATATCGATACATTCTAGGTTTTAACCCAGATGTATCGATACAT
141583 TTCTCA
66 TTCTCA
*
141589 ATGTATCGATACATTC
1 TTGTATCGATACATTC
141605 ATGCATTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
70 39 0.51
71 37 0.49
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.44
Consensus pattern (71 bp):
TTGTATCGATACATTCTTCATTATATCGATACATTCTAGGTTTTAACCCAGATGTATCGATACAT
TTCTCA
Found at i:141594 original size:20 final size:21
Alignment explanation
Indices: 141564--141603 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
141554 TGGGTTTTAA
141564 CTCAGATGTATCGATACATTT
1 CTCAGATGTATCGATACATTT
141585 CTCA-ATGTATCGATACATT
1 CTCAGATGTATCGATACATT
141604 CATGCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (21 bp):
CTCAGATGTATCGATACATTT
Found at i:144255 original size:13 final size:13
Alignment explanation
Indices: 144237--144262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
144227 TACACAAAGT
144237 ATGTATCGATACA
1 ATGTATCGATACA
144250 ATGTATCGATACA
1 ATGTATCGATACA
144263 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:144260 original size:32 final size:33
Alignment explanation
Indices: 144219--144282 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
144209 TAGCCAAACT
**
144219 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
144251 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
144283 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:144784 original size:34 final size:35
Alignment explanation
Indices: 144721--144787 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
144711 CTAAGTGATT
144721 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
144757 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
144788 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:148019 original size:13 final size:13
Alignment explanation
Indices: 148001--148025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147991 TTTTCCAGAT
148001 TGTATCGATACAA
1 TGTATCGATACAA
148014 TGTATCGATACA
1 TGTATCGATACA
148026 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:148875 original size:30 final size:32
Alignment explanation
Indices: 148839--148906 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
148829 GGGTGACAAC
* *
148839 GTATTAAGGGGGAGAGTTTGTATAAA-TTTT-
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
148869 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
148901 GTATTA
1 GTATTA
148907 GTTGCATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 24 0.71
31 4 0.12
32 6 0.18
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (32 bp):
GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
Found at i:150047 original size:13 final size:13
Alignment explanation
Indices: 150029--150054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150019 TACACAAAGT
150029 ATGTATCGATACA
1 ATGTATCGATACA
150042 ATGTATCGATACA
1 ATGTATCGATACA
150055 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:150052 original size:32 final size:33
Alignment explanation
Indices: 150011--150074 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
150001 TAGCCAAACT
**
150011 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
150043 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
150075 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:150575 original size:34 final size:35
Alignment explanation
Indices: 150512--150578 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
150502 CTAAGTGATT
150512 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
150548 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
150579 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:151161 original size:78 final size:79
Alignment explanation
Indices: 150930--151180 Score: 278
Period size: 78 Copynumber: 3.2 Consensus size: 79
150920 TTATTCATGT
* *
150930 TTTTATTTTTAAAATACCGATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTCG-AGGAG
1 TTTTATTTTCAAAATACCGATTTTTCACAATCGGAGATACTCCAACCCTGTTATTTTCGAAGG-G
* *
150994 ATACTCTAACTCCAG
65 ATACTCTAACCCCAA
* * * * * *
151009 TTTTA-TTTCTAGAACACCAATTTTTCATAATCGAAGATACTCCAACCCTGTTATTTT-GAGGGG
1 TTTTATTTTC-AAAATACCGATTTTTCACAATCGGAGATACTCCAACCCTGTTATTTTCGAAGGG
*
151072 AGACTCTAACCCCAA
65 ATACTCTAACCCCAA
*
151087 TTTTATTTTCAAAATACCGATTTTTCACAATCGG-GAATACTCTAACCC-GTTATTTTCGAAGGG
1 TTTTATTTTCAAAATACCGATTTTTCACAATCGGAG-ATACTCCAACCCTGTTATTTTCGAAGGG
* * **
151150 ATACGCCAACCCCGT
65 ATACTCTAACCCCAA
* *
151165 TTTTATCTCCAAAATA
1 TTTTATTTTCAAAATA
151181 TTAAATTTTT
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
77 9 0.06
78 81 0.57
79 52 0.37
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTTATTTTCAAAATACCGATTTTTCACAATCGGAGATACTCCAACCCTGTTATTTTCGAAGGGA
TACTCTAACCCCAA
Found at i:155414 original size:79 final size:79
Alignment explanation
Indices: 155231--155839 Score: 556
Period size: 78 Copynumber: 7.7 Consensus size: 79
155221 GAGATAGTGG
* * * * * * *
155231 GGTTGGAGTATCCCCGAAGAT-AGAAATTTAATGTTTTTAGAAGTAAAGACGGGGTTAGAGTATC
1 GGTTGGAGTATCCCCG-AGATGAAAAATTTAATATTTTGA-AAATAAAAATGAGGTTAGAGTATC
* *
155295 CCCTCGAAAATAGC-A
64 CCTTCGAAAATAACGA
* * * * * * * * * *
155310 GGGGTGGAATATCCCTGCGATAAAAAACTTAATATTTTGGAGATAAAAACGGGGTTAGAGTAT-C
1 -GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTATCC
*
155374 CTTCAAAAATAACGA
65 CTTCGAAAATAACGA
* * ** * *
155389 AGTTAGAGTATCCCCTCGATGAAAAATTTAACATTTTGAAAAT-AAAATGGGGTTAGAGTATCTC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTATC-C
* *
155453 C-TCGAAAATAATGG
65 CTTCGAAAATAACGA
* * *
155467 GGTTGGAGTATCCCCGAGATGGAAAA-TTAATATTTTGAAAATAAAAATGAGGTTGGAATATCCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTATCCC
* **
155531 CTCGAAAATAATAA
66 TTCGAAAATAACGA
* * * *
155545 GGTTAGAGTATCTCCGAGATGAAAAA-TTAATATTTTAAAAATAAAAATGAGGTTGGAGTATTCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTA-TCC
* *
155609 CTT-GAAAACAACGG
65 CTTCGAAAATAACGA
** * * * * *
155623 GGTTGGAGTATCTTCAAGATGAAAATTTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATTCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTA-TCC
*
155688 CTT-AAAAATAACGA
65 CTTCGAAAATAACGA
* ** * * *
155702 GGTTGGAATATCCCTAAGATAAAAAATTTAATATTGTT-AAAATAAAAACGAGATTAGAGTATCC
1 GGTTGGAGTATCCCCGAGATGAAAAATTTAATATT-TTGAAAATAAAAATGAGGTTAGAGTATCC
* **
155766 ATTCTTAAATAACG-
65 CTTCGAAAATAACGA
155780 GGATTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAG
1 GG-TTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAG
155840 AGTATCATCG
Statistics
Matches: 436, Mismatches: 81, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
77 34 0.08
78 194 0.44
79 180 0.41
80 28 0.06
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTTAGAGTATCCC
TTCGAAAATAACGA
Found at i:156004 original size:131 final size:128
Alignment explanation
Indices: 155772--156101 Score: 396
Period size: 131 Copynumber: 2.5 Consensus size: 128
155762 ATCCATTCTT
*
155772 AAATAAC-GGGATTGGAGTATCCCCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGAGGTT
1 AAATAACAGGG-TTGGAGTATCCCC-A-ATG-AAAATTTAATATTTTGAAAATAAAAACG-GGTT
* * * * *
155836 -AGAGAGTATCATCGATGGTGAAAAATCGATATTTTGGAAGTAAAAATAGGGTTGGAGTATCTCT
61 GA-AAAGTATCACCGATAGTGAAAAATCGATATGTTGGAAGTAAAAATAGGGTTGGAGTATCTCC
**
155900 TTGA
125 TCAA
* *
155904 AAATAACAGGGTTGGAGTATCTCCACAATGAAATTTTAATATTTTGGAAATAAAAACGGGATTGA
1 AAATAACAGGGTTGGAGTATC-CC-CAATGAAAATTTAATATTTTGAAAATAAAAACGGG-TTGA
* *
155969 AAAGTATCGCCGATAGT-AAAAGATTGATATGTTGGAAGTAAAAATAGGGTTGGAGTATCTCCTC
63 AAAGTATCACCGATAGTGAAAA-ATCGATATGTTGGAAGTAAAAATAGGGTTGGAGTATCTCCTC
156033 AA
127 AA
* *
156035 AAATAACAGGATTGGAGTATCCCCGTGATGAAAATTTAATATTTTGAAAATAAAAACGGGGTTGA
1 AAATAACAGGGTTGGAGTATCCCC--AATGAAAATTTAATATTTTGAAAATAAAAAC-GGGTTGA
156100 AA
63 AA
156102 TATCCCCTCG
Statistics
Matches: 173, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
129 1 0.01
130 8 0.05
131 133 0.77
132 24 0.14
133 6 0.03
134 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (128 bp):
AAATAACAGGGTTGGAGTATCCCCAATGAAAATTTAATATTTTGAAAATAAAAACGGGTTGAAAA
GTATCACCGATAGTGAAAAATCGATATGTTGGAAGTAAAAATAGGGTTGGAGTATCTCCTCAA
Found at i:158342 original size:53 final size:51
Alignment explanation
Indices: 158266--158405 Score: 199
Period size: 51 Copynumber: 2.7 Consensus size: 51
158256 AATAGCTTAC
* * * *
158266 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGATCAAAAAATTCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGATC--AAAACTCAAA
* * *
158319 ATGTATCGATACAATGAATAATGTATTGATAAATTTGGATCAAAACTCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGATCAAAACTCAAA
158370 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
158406 TCTTTTCAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 41 0.53
53 37 0.47
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTGGATCAAAACTCAAA
Found at i:160325 original size:21 final size:21
Alignment explanation
Indices: 160301--160343 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
160291 ACACTTTAAG
160301 AGAAAAATAGTATAAAATTTT
1 AGAAAAATAGTATAAAATTTT
* * *
160322 AGAAAAATCGTTTAGAATTTT
1 AGAAAAATAGTATAAAATTTT
160343 A
1 A
160344 AAATGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (21 bp):
AGAAAAATAGTATAAAATTTT
Found at i:161840 original size:22 final size:21
Alignment explanation
Indices: 161791--161866 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 21
161781 AAAAACCCAG
* * *
161791 AATGTATCGATATAA-TGAGA
1 AATGTATCGATACAATTTAGC
161811 AATGTATCGATACAATTATAAGC
1 AATGTATCGATACAATT-T-AGC
*
161834 -ATGTATCTATAC-ATTTAGC
1 AATGTATCGATACAATTTAGC
161853 AATGTATCGATACA
1 AATGTATCGATACA
161867 TTTCCTTGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.07
20 26 0.57
21 4 0.09
22 11 0.24
23 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACAATTTAGC
Found at i:165687 original size:66 final size:66
Alignment explanation
Indices: 165578--165712 Score: 209
Period size: 66 Copynumber: 2.0 Consensus size: 66
165568 TACCATTCCT
* *
165578 GAGGGTTCCATATAACTCATATTCGAAAATCGTAACTCCTTTATCTTAGCTTTTCTTGAGGCAAA
1 GAGGGTTCCATATAACTCATATTCGAAAATCATAACTCCTTTATCTTAGCTTTTCTCGAGGCAAA
165643 C
66 C
* * *
165644 GAGGGTTCCATAT-AGTGCATATTTGAAAATCATAACTCTTTTATCTTAGCTTTTCTCGAGGCAA
1 GAGGGTTCCATATAACT-CATATTCGAAAATCATAACTCCTTTATCTTAGCTTTTCTCGAGGCAA
165708 AC
65 AC
165710 GAG
1 GAG
165713 TGCTCTTTGG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 2 0.03
66 61 0.97
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (66 bp):
GAGGGTTCCATATAACTCATATTCGAAAATCATAACTCCTTTATCTTAGCTTTTCTCGAGGCAAA
C
Found at i:169576 original size:14 final size:14
Alignment explanation
Indices: 169557--169594 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
169547 TACATGAACC
169557 TATTTTTTAAATTT
1 TATTTTTTAAATTT
169571 TATTTTTTAAATTT
1 TATTTTTTAAATTT
*
169585 AATATTTTTA
1 TAT-TTTTTA
169595 TCTATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTAAATTT
Found at i:169585 original size:13 final size:13
Alignment explanation
Indices: 169557--169608 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
169547 TACATGAACC
169557 TATTTTTTAAATTT
1 TATTTTTTAAA-TT
169571 TATTTTTTAAATT
1 TATTTTTTAAATT
** *
169584 TAATATTTTTATCTA
1 T-AT-TTTTTAAATT
169599 TATTTTTTAA
1 TATTTTTTAA
169609 TATTAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 9 0.28
14 15 0.47
15 8 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTTTAAATT
Found at i:169622 original size:19 final size:18
Alignment explanation
Indices: 169600--169635 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
169590 TTTTATCTAT
*
169600 ATTTTTTAATATTAAATAA
1 ATTTTTAAAT-TTAAATAA
169619 ATTTTTAAATTTAAATA
1 ATTTTTAAATTTAAATA
169636 TATAACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTAAATTTAAATAA
Found at i:169798 original size:27 final size:27
Alignment explanation
Indices: 169763--169934 Score: 106
Period size: 30 Copynumber: 6.1 Consensus size: 27
169753 TAGATAATAT
169763 TAAATATAATTAAAAAATATAATATAAA
1 TAAA-ATAATTAAAAAATATAATATAAA
*
169791 TAAAATAATTAAAATATAATATTATATTATAA
1 TAAAATAATT-AAA-A-AATATAATA-TA-AA
* *
169823 TAATATAATTTAAAATATATAATATAAA
1 TAAAATAA-TTAAAAAATATAATATAAA
*
169851 TTATAAATATATT--AAAAT-TTATATAAA
1 -TA-AAATA-ATTAAAAAATATAATATAAA
169878 TAAAA-AATTTAAATATAATTATAATAT-AA
1 TAAAATAA-TTAAA-A-AA-TATAATATAAA
* *
169907 TAAAA-AA-TATATAAATATAATTTAAA
1 TAAAATAATTA-AAAAATATAATATAAA
169933 TA
1 TA
169935 TATAAATTAT
Statistics
Matches: 116, Mismatches: 10, Indels: 38
0.71 0.06 0.23
Matches are distributed among these distances:
23 1 0.01
24 3 0.03
25 10 0.09
26 9 0.08
27 18 0.16
28 16 0.14
29 15 0.13
30 26 0.22
31 4 0.03
32 12 0.10
33 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAAATAATTAAAAAATATAATATAAA
Found at i:169828 original size:46 final size:44
Alignment explanation
Indices: 169778--169944 Score: 138
Period size: 46 Copynumber: 3.8 Consensus size: 44
169768 ATAATTAAAA
169778 AATATAATATAAATAAAATAATTAAAATATAATATTATATTATAAT
1 AATATAATATAAATAAAATAATTAAAATATAA-ATTATA-TATAAT
* * *
169824 AATATAATTTAAA-ATATATAATATAAATTATAAA-TATAT-TAA-
1 AATATAATATAAATA-AAATAAT-TAAAATATAAATTATATATAAT
* *
169866 AAT-TTATATAAATAAAA-AATTTAAATAT-AATTATAATATAAT
1 AATATAATATAAATAAAATAATTAAAATATAAATTAT-ATATAAT
*
169908 AA-A-AA-ATATATAAATATAATTTAAATATATAAATTAT
1 AATATAATATAAATAAA-ATAA-TTAAA-ATATAAATTAT
169945 CACTCATCCA
Statistics
Matches: 97, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
38 2 0.02
39 9 0.09
40 13 0.13
41 14 0.14
42 8 0.08
43 7 0.07
44 5 0.05
45 11 0.11
46 19 0.20
47 9 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (44 bp):
AATATAATATAAATAAAATAATTAAAATATAAATTATATATAAT
Found at i:170771 original size:20 final size:20
Alignment explanation
Indices: 170742--170780 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
170732 AATAAAAAAT
*
170742 TAATTTAAAT-TATTATTTAA
1 TAATTAAAATATATT-TTTAA
170762 TAATTAAAATATATTTTTA
1 TAATTAAAATATATTTTTA
170781 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTAAAATATATTTTTAA
Found at i:171414 original size:20 final size:20
Alignment explanation
Indices: 171391--171431 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
171381 AAATAAATAT
171391 TAAATATA-ATATATATTTAA
1 TAAATATATATATA-ATTTAA
*
171411 TAAATATATATTTAATTTAA
1 TAAATATATATATAATTTAA
171431 T
1 T
171432 GATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATATATATAATTTAA
Found at i:171678 original size:14 final size:14
Alignment explanation
Indices: 171659--171686 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
171649 TTCATTGGTG
171659 TATATATATAATTA
1 TATATATATAATTA
171673 TATATATATAATTA
1 TATATATATAATTA
171687 ATTAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATATAATTA
Found at i:172681 original size:9 final size:9
Alignment explanation
Indices: 172646--172692 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
172636 ATATAAAAAT
172646 ATAAATATA
1 ATAAATATA
172655 ATATAATATA
1 ATA-AATATA
*
172665 TTTAAATATA
1 -ATAAATATA
172675 ATAAATATA
1 ATAAATATA
*
172684 ATAGATATA
1 ATAAATATA
172693 TTAATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 19 0.58
10 12 0.36
11 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAAATATA
Found at i:172691 original size:26 final size:27
Alignment explanation
Indices: 172642--172701 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 27
172632 CATAATATAA
172642 AAATATAAATATAATATAATATAT-TT
1 AAATATAAATATAATATAATATATATT
172668 AAATAT-AATA-AATATAATAGATATATT
1 AAATATAAATATAATATAAT--ATATATT
172695 AATATAT
1 AA-ATAT
172702 TTTATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 8 0.27
25 4 0.13
26 10 0.33
27 4 0.13
28 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATATAAATATAATATAATATATATT
Found at i:172703 original size:36 final size:34
Alignment explanation
Indices: 172635--172703 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 34
172625 ATTTTAACAT
*
172635 AATATAAAAATATAAATATAATATAATATATTTA
1 AATATAAAAATATAAAGATAATATAATATATTTA
172669 AATATAATAAATATAATAGAT-ATATTAATATATTT
1 AATATAA-AAATATAA-AGATAATA-TAATATATTT
172704 TATTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 7 0.23
35 11 0.35
36 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (34 bp):
AATATAAAAATATAAAGATAATATAATATATTTA
Found at i:172745 original size:17 final size:16
Alignment explanation
Indices: 172706--172749 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
172696 ATATATTTTA
172706 TTTATATTT-AAAATT
1 TTTATATTTAAAAATT
172721 TTAATATATTTAAATAATT
1 TT--TATATTTAAA-AATT
172740 TTTATATTTA
1 TTTATATTTA
172750 TATTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
17 15 0.60
18 2 0.08
19 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATATTTAAAAATT
Found at i:172751 original size:23 final size:22
Alignment explanation
Indices: 172704--172760 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
172694 TAATATATTT
172704 TATTTATATTT-AA-AATTTTA
1 TATTTATATTTAAATAATTTTA
172724 -A--TATATTTAAATAATTTTTA
1 TATTTATATTTAAATAA-TTTTA
*
172744 TATTTATATTTATATAA
1 TATTTATATTTAAATAA
172761 ATAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 7 0.23
18 2 0.07
19 3 0.10
20 5 0.17
21 1 0.03
23 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTATATTTAAATAATTTTA
Found at i:173203 original size:30 final size:31
Alignment explanation
Indices: 173145--173203 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
173135 TAATTTTCCT
**
173145 TTTTTTTTAATTCTAAAATAATAAATTTAAA
1 TTTTTTTTAATAATAAAATAATAAATTTAAA
*
173176 TTTTTTTTAATAATAAAAT-ATATATTTA
1 TTTTTTTTAATAATAAAATAATAAATTTA
173204 TATATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTTTTTTAATAATAAAATAATAAATTTAAA
Found at i:173409 original size:18 final size:18
Alignment explanation
Indices: 173388--173438 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
173378 TATATATTTT
*
173388 TAAAAATATATTTAAAAA
1 TAAAAATATATATAAAAA
173406 TAAAAAT-TAATATAAAAA
1 TAAAAATAT-ATATAAAAA
173424 TAAAACATATA-ATAA
1 TAAAA-ATATATATAA
173439 TCTTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 1 0.03
18 24 0.83
19 3 0.10
20 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATATATATAAAAA
Found at i:173721 original size:18 final size:19
Alignment explanation
Indices: 173685--173722 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
173675 TAAAATATTA
**
173685 ATTTTATAATTTTTTACAT
1 ATTTTATAATTTTAAACAT
173704 ATTTT-TAATTTTAAACAT
1 ATTTTATAATTTTAAACAT
173722 A
1 A
173723 ACATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTATAATTTTAAACAT
Found at i:173764 original size:13 final size:14
Alignment explanation
Indices: 173737--173800 Score: 66
Period size: 13 Copynumber: 4.9 Consensus size: 14
173727 AAAAATACGA
173737 ATTTAATATAATAT
1 ATTTAATATAATAT
173751 ATTTAATA-AATAT
1 ATTTAATATAATAT
*
173764 A---AAAATAATAT
1 ATTTAATATAATAT
*
173775 A-TAAATATAATAT
1 ATTTAATATAATAT
173788 ATTTAAATATAAT
1 ATTT-AATATAAT
173801 TAAAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
13 16 0.38
14 9 0.21
15 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTAATATAATAT
Found at i:173789 original size:15 final size:15
Alignment explanation
Indices: 173740--173800 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
173730 AATACGAATT
* *
173740 TAATATA-ATATATT
1 TAATATATATAAATA
* *
173754 TAATAAATATAAAAA
1 TAATATATATAAATA
173769 T-A-ATATATAAATA
1 TAATATATATAAATA
*
173782 TAATATATTTAAATA
1 TAATATATATAAATA
173797 TAAT
1 TAAT
173801 TAAAATAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.27
14 8 0.22
15 19 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATATATAAATA
Found at i:173795 original size:26 final size:26
Alignment explanation
Indices: 173737--173804 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 26
173727 AAAAATACGA
*
173737 ATTTAATATAATATATTTAATAAATAT
1 ATTTAA-ATAATATATTAAATAAATAT
*
173764 A--AAAATAATATA-TAAATATAATAT
1 ATTTAAATAATATATTAAATA-AATAT
173788 ATTTAAAT-ATA-ATTAAA
1 ATTTAAATAATATATTAAA
173805 ATAATACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
23 5 0.15
24 15 0.44
25 9 0.26
26 4 0.12
27 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTAAATAATATATTAAATAAATAT
Found at i:173878 original size:6 final size:6
Alignment explanation
Indices: 173867--173891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
173857 TTTAAATATT
173867 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
173892 AAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:174946 original size:15 final size:16
Alignment explanation
Indices: 174926--174964 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
174916 CAAAAATAAA
*
174926 AATATATTTAT-ATAT
1 AATATATTAATAATAT
174941 AATATATTAATAATAT
1 AATATATTAATAATAT
174957 ATATATAT
1 A-ATATAT
174965 CTATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 5 0.24
17 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATATTAATAATAT
Found at i:176567 original size:2 final size:2
Alignment explanation
Indices: 176560--176603 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
176550 TGATATAAAG
176560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176602 AT
1 AT
176604 GCTGGAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178029 original size:18 final size:16
Alignment explanation
Indices: 178006--178057 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
177996 ATCTATAAAT
178006 AAATTAAAAATAATATAA
1 AAATTAAAAAT-AT-TAA
*
178024 AAATTATAAATATT-A
1 AAATTAAAAATATTAA
*
178039 AAATTTAAAAT-TTAA
1 AAATTAAAAATATTAA
178054 AAAT
1 AAAT
178058 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.07
15 15 0.50
16 1 0.03
17 2 0.07
18 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAAAATATTAA
Found at i:178032 original size:14 final size:14
Alignment explanation
Indices: 178015--178082 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
178005 TAAATTAAAA
178015 ATAATATAAAAATT
1 ATAATATAAAAATT
*
178029 ATAAATATTAAAATTT
1 AT-AATA-TAAAAATT
* *
178045 AAAATTTAAAAA-T
1 ATAATATAAAAATT
178058 A-AAT-TAAAAATT
1 ATAATATAAAAATT
* *
178070 ATATTTTAAAAAT
1 ATAATATAAAAAT
178083 GACTATCGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.14
12 5 0.11
13 4 0.09
14 14 0.32
15 7 0.16
16 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAAAATT
Found at i:178077 original size:25 final size:25
Alignment explanation
Indices: 178035--178082 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
178025 AATTATAAAT
*
178035 ATTAAAATTTAAAATTTAAAAATAA
1 ATTAAAAATTAAAATTTAAAAATAA
* *
178060 ATTAAAAATTATATTTTAAAAAT
1 ATTAAAAATTAAAATTTAAAAAT
178083 GACTATCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTAAAAATTAAAATTTAAAAATAA
Found at i:178918 original size:14 final size:14
Alignment explanation
Indices: 178896--178956 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
178886 AATATGATGT
*
178896 AATTGTTTTATATA
1 AATTTTTTTATATA
*
178910 AATTTTTTTTTATA
1 AATTTTTTTATATA
* *
178924 ATATATATTTTATACA
1 A-AT-TTTTTTATATA
*
178940 AATTTTTTAAT-TA
1 AATTTTTTTATATA
178953 AATT
1 AATT
178957 AGTATTACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
13 5 0.14
14 19 0.51
15 4 0.11
16 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
AATTTTTTTATATA
Found at i:179803 original size:31 final size:30
Alignment explanation
Indices: 179752--179812 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
179742 AAATATAAAG
* *
179752 CAAAAAATGCAAACATAAATTGATTCAATT
1 CAAAAAATACAAACATAAATTAATTCAATT
* *
179782 CAAAATAATACAAATATAAATTAATTTAATT
1 CAAAA-AATACAAACATAAATTAATTCAATT
179813 TTAATTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (30 bp):
CAAAAAATACAAACATAAATTAATTCAATT
Found at i:180341 original size:14 final size:15
Alignment explanation
Indices: 180322--180354 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
180312 AATAAGATTA
*
180322 TAAATTTAT-TATTT
1 TAAATTAATATATTT
180336 TAAATTAATATATTT
1 TAAATTAATATATTT
180351 TAAA
1 TAAA
180355 ATATTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTAATATATTT
Found at i:180781 original size:2 final size:2
Alignment explanation
Indices: 180776--180804 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
180766 TCTTCAAACA
180776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
180805 AACCGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:181482 original size:18 final size:20
Alignment explanation
Indices: 181455--181495 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
181445 TTTTAATTAC
181455 TATTTATTTAA-TA-AAAAA
1 TATTTATTTAATTATAAAAA
*
181473 TATTTTTTTAATTATAAAAA
1 TATTTATTTAATTATAAAAA
181493 TAT
1 TAT
181496 AAAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTATTTAATTATAAAAA
Found at i:181510 original size:14 final size:14
Alignment explanation
Indices: 181491--181521 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
181481 TAATTATAAA
181491 AATATAAAAATTTT
1 AATATAAAAATTTT
181505 AATATAAAAATTTT
1 AATATAAAAATTTT
181519 AAT
1 AAT
181522 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATAAAAATTTT
Found at i:181531 original size:23 final size:23
Alignment explanation
Indices: 181476--181544 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
181466 TAAAAAATAT
* * *
181476 TTTTTTAATTATAAAAATATAAA
1 TTTTTTAAATATAAAAATTTTAA
**
181499 AATTTT-AATATAAAAATTTTAA
1 TTTTTTAAATATAAAAATTTTAA
*
181521 TTTTTTAAATAATAAAAAATTTAA
1 TTTTTTAAAT-ATAAAAATTTTAA
181545 AAAATTTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 17 0.47
23 7 0.19
24 12 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTTTTAAATATAAAAATTTTAA
Found at i:181543 original size:24 final size:22
Alignment explanation
Indices: 181501--181544 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
181491 AATATAAAAA
*
181501 TTTTAATATAAAAATTTTAATT
1 TTTTAATATAAAAAATTTAATT
181523 TTTTAAATAATAAAAAATTTAA
1 TTTT-AAT-ATAAAAAATTTAA
181545 AAAATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAATATAAAAAATTTAATT
Found at i:185506 original size:13 final size:13
Alignment explanation
Indices: 185488--185513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
185478 ATTTACCTGC
185488 ATGTATCGATACA
1 ATGTATCGATACA
185501 ATGTATCGATACA
1 ATGTATCGATACA
185514 TTTGAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:185591 original size:33 final size:33
Alignment explanation
Indices: 185554--185620 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
185544 AGTAGCTTAA
*
185554 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
* ***
185587 ATTGTATCAATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
185620 A
1 A
185621 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCAATACAAAAAAATATGTATCGATAC
Found at i:189558 original size:20 final size:19
Alignment explanation
Indices: 189529--189602 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
189519 TTTATCTAGA
*
189529 TGTATTGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
189549 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
* *
189569 TGTATCGATATATTTTACAA
1 TGTATCGATACATTTT-CAT
189589 TGTATCGATACATT
1 TGTATCGATACATT
189603 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:191982 original size:51 final size:51
Alignment explanation
Indices: 191927--192038 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
191917 TCCCGGTTCC
** ** * *
191927 ATTTCCAAAACATCAATTTTTCTTAATCGGGGATATTCCAACTCTGATTTT
1 ATTTCCAAAACATCAATTTACCGCAATCAGGGATACTCCAACTCTGATTTT
** * *
191978 ATTTCTGAAGCATCGATTTACCGCAATCAGGGATACTCCAACTCTGATTTT
1 ATTTCCAAAACATCAATTTACCGCAATCAGGGATACTCCAACTCTGATTTT
192029 ATTTCCAAAA
1 ATTTCCAAAA
192039 TACTAATTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTACCGCAATCAGGGATACTCCAACTCTGATTTT
Found at i:192119 original size:28 final size:28
Alignment explanation
Indices: 192057--192127 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
192047 TTTCAAAATT
* *
192057 GGGGAAACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCATA
192085 GGGGATACTCCAACCCCGTTATTTC-TAA
1 GGGGATACTCCAACCCCGTTATTTCAT-A
* *
192113 GGTGATACTCTAACC
1 GGGGATACTCCAACC
192128 TTGGCTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCATA
Found at i:192212 original size:28 final size:28
Alignment explanation
Indices: 192170--192237 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
192160 TAATCTGGGG
192170 TACTCCAA-CCTCGTTATTTCATCGA-GGA
1 TACTCCAATCCTCGTTATTTC--CGACGGA
192198 TACTCCAATCC-CGTTATTTCCGAGCGGA
1 TACTCCAATCCTCGTTATTTCCGA-CGGA
192226 TACTCCAATCCT
1 TACTCCAATCCT
192238 GATTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.08
28 31 0.86
29 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (28 bp):
TACTCCAATCCTCGTTATTTCCGACGGA
Found at i:192252 original size:108 final size:105
Alignment explanation
Indices: 192006--192285 Score: 319
Period size: 108 Copynumber: 2.6 Consensus size: 105
191996 TACCGCAATC
*
192006 AGGGATACTCCAACTCTGATTTTATTTCCAAAATACTAATTTTTCAAAATTGGGGAAACTCCAAC
1 AGGGATACTCCAAC-CTGATTTTATTTCTAAAATACTAATTTTTCAAAATTGGGGAAACTCCAAC
* *
192071 CCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCTA
65 CCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCA
* ** * * * * *
192112 AGGTGATACTCTAACCTTGGCTTTATATCTAAAATATTGATTTTCTCATAATCTGGGG-TACTCC
1 AGG-GATACTCCAACC-TGATTTTATTTCTAAAATACTAATTTT-TCAAAAT-TGGGGAAACTCC
* * *
192176 AACCTCGTTATTTCATCGAGGATACTCCAATCCCGTTATTTCCG
62 AACCCCGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCA
* * * * *
192220 AGCGGATACTCCAATCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 AG-GGATACTCCAA-CCTGATTTTATTTCTAAAATACTAATTTTTCAAAATTGGGGAAACTCCAA
192285 C
64 C
192286 TCCGATTTTA
Statistics
Matches: 143, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
106 7 0.05
107 46 0.32
108 82 0.57
109 8 0.06
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (105 bp):
AGGGATACTCCAACCTGATTTTATTTCTAAAATACTAATTTTTCAAAATTGGGGAAACTCCAACC
CCGTTATTTCATCGAGGATACTCCAACCCCGTTATTTCCA
Found at i:192388 original size:51 final size:50
Alignment explanation
Indices: 192223--192388 Score: 188
Period size: 51 Copynumber: 3.3 Consensus size: 50
192213 ATTTCCGAGC
* * * * * *
192223 GGATACTCCAATCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCT-AAATATCGATTTTTCATAATCGG
* * * *
192274 GGATACTCCAACTCCGATTTTATTTCCAAAATATTGATTTCTCATAATCGG
1 GGATACTCCAACCCCGATTTTATTT-CTAAATATCGATTTTTCATAATCGG
* * *
192325 GGATACTTCAACCCCGGTCTTATTTCTAAATCATCGATTTTTCATAATCGG
1 GGATACTCCAACCCCGATTTTATTTCTAAAT-ATCGATTTTTCATAATCGG
192376 GGATACTCCAACC
1 GGATACTCCAACC
192389 TTGTTATTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
50 5 0.05
51 89 0.94
52 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (50 bp):
GGATACTCCAACCCCGATTTTATTTCTAAATATCGATTTTTCATAATCGG
Found at i:192459 original size:79 final size:78
Alignment explanation
Indices: 192323--192546 Score: 297
Period size: 79 Copynumber: 2.8 Consensus size: 78
192313 TCTCATAATC
* * * * *
192323 GGGGATACTTCAACCCCGGTCTTA-TTTCTAAATCATCGATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAAT-ACCGATTTTT-ATAATCGAGGATACTCCAA
*
192387 CCTTGTTATTTTTGA
64 CCCTGTTATTTTTGA
* * *
192402 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTGCTATAATCAAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAATACCGATTT-TTATAATCGAGGATACTCCAAC
192467 CCTGTTATTTTTGA
65 CCTGTTATTTTTGA
*** *
192481 GGGGATACTCCAACCCCGGTTTTATTTTTGGAACACCGATTTTTATAATCGAGGATACTCCAACC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAATACCGATTTTTATAATCGAGGATACTCCAACC
192546 C
66 C
192547 CGTTGTTATC
Statistics
Matches: 127, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
78 22 0.17
79 96 0.76
80 9 0.07
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGGTTTTATTTTCAAAATACCGATTTTTATAATCGAGGATACTCCAACC
CTGTTATTTTTGA
Found at i:193952 original size:62 final size:62
Alignment explanation
Indices: 193855--193997 Score: 268
Period size: 62 Copynumber: 2.3 Consensus size: 62
193845 TATCCGCCTT
* *
193855 CGTGAGTATCCCTCCGTATAGGCATGGCAATACCTTCCGAGATGTAAATTACCTATGTCTCA
1 CGTGAGTAACCCTCCGCATAGGCATGGCAATACCTTCCGAGATGTAAATTACCTATGTCTCA
193917 CGTGAGTAACCCTCCGCATAGGCATGGCAATACCTTCCGAGATGTAAATTACCTATGTCTCA
1 CGTGAGTAACCCTCCGCATAGGCATGGCAATACCTTCCGAGATGTAAATTACCTATGTCTCA
193979 CGTGAGTAACCCTCCGCAT
1 CGTGAGTAACCCTCCGCAT
193998 TTACATAGGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 79 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (62 bp):
CGTGAGTAACCCTCCGCATAGGCATGGCAATACCTTCCGAGATGTAAATTACCTATGTCTCA
Found at i:199340 original size:290 final size:290
Alignment explanation
Indices: 198820--199404 Score: 1089
Period size: 290 Copynumber: 2.0 Consensus size: 290
198810 AAGCTTTTGT
198820 AAAAGTGGGATTAGTGAGCCAGAGAGAAAAAGTCGTAGGATCATCCTATTGCTACTGCAATCAGG
1 AAAAGTGGGATTAGTGAGCCAGAGAGAAAAAGTCGTAGGATCATCCTATTGCTACTGCAATCAGG
198885 CACATGATTTGCAGCAATGCCCATCATTCCTAAAGAAGGTCCAATGGATGATGGATCGATCAGAA
66 CACATGATTTGCAGCAATGCCCATCATTCCTAAAGAAGGTCCAATGGATGATGGATCGATCAGAA
*
198950 ATTGAATTCTATGAAGAATATGATGAACGAATTAGTGAGTCTATTAATGCATTAGAAGAATGAAG
131 ATTGAATTCTATGAAGAATATGATGAACGAATTAGTGAGTCTATTAATGCATTAGAAGAACGAAG
* *
199015 AACTAATGAAGATGGGGTCTTGATGTGTCTCTCCCTCATAGGTATAGAAAAGAGACTTGACGAAA
196 AACTAATGAAGATGGGGTCCTAATGTGTCTCTCCCTCATAGGTATAGAAAAGAGACTTGACGAAA
*
199080 GCTTTTAATGTTATGCCTCGAGGTGGATGG
261 GCTTTCAATGTTATGCCTCGAGGTGGATGG
* *
199110 AAAAGTGGGATTAGTGAGCCAGAGAGAAGAAGTCGTGGGATCATCCTATTGCTACTGCAATCAGG
1 AAAAGTGGGATTAGTGAGCCAGAGAGAAAAAGTCGTAGGATCATCCTATTGCTACTGCAATCAGG
*
199175 CACATGATTTGCAGCAATGCCCATCATTCCTAAAGAAGGTCCAATGGATGATGGATCGATTAGAA
66 CACATGATTTGCAGCAATGCCCATCATTCCTAAAGAAGGTCCAATGGATGATGGATCGATCAGAA
199240 ATTGAATTCTATGAAGAATATGATGAACGAATTAGTGAGTCTATTAATGCATTAGAAGAACGAAG
131 ATTGAATTCTATGAAGAATATGATGAACGAATTAGTGAGTCTATTAATGCATTAGAAGAACGAAG
*
199305 AACTAATGAAGATGGGGTCCTAATGTGTCTCTCCCTCATGGGTATAGAAAAGAGACTTGACGAAA
196 AACTAATGAAGATGGGGTCCTAATGTGTCTCTCCCTCATAGGTATAGAAAAGAGACTTGACGAAA
*
199370 GCTTTCGATGTTATGCCTCGAGGTGGATGG
261 GCTTTCAATGTTATGCCTCGAGGTGGATGG
199400 AAAAG
1 AAAAG
199405 GCCGCCTAGA
Statistics
Matches: 286, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
290 286 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (290 bp):
AAAAGTGGGATTAGTGAGCCAGAGAGAAAAAGTCGTAGGATCATCCTATTGCTACTGCAATCAGG
CACATGATTTGCAGCAATGCCCATCATTCCTAAAGAAGGTCCAATGGATGATGGATCGATCAGAA
ATTGAATTCTATGAAGAATATGATGAACGAATTAGTGAGTCTATTAATGCATTAGAAGAACGAAG
AACTAATGAAGATGGGGTCCTAATGTGTCTCTCCCTCATAGGTATAGAAAAGAGACTTGACGAAA
GCTTTCAATGTTATGCCTCGAGGTGGATGG
Found at i:205284 original size:7 final size:7
Alignment explanation
Indices: 205272--205319 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
205262 CCCACTTTTA
205272 AAAAAAC
1 AAAAAAC
205279 AAAAAAAC
1 -AAAAAAC
205287 AAAAAAC
1 AAAAAAC
205294 AAAAAAC
1 AAAAAAC
*
205301 AAAACAAA
1 AAAA-AAC
205309 AACAAAAC
1 AA-AAAAC
205317 AAA
1 AAA
205320 GAAAAAAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 19 0.53
8 15 0.42
9 2 0.06
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:205311 original size:11 final size:11
Alignment explanation
Indices: 205273--205319 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
205263 CCACTTTTAA
205273 AAAAACAAAA-
1 AAAAACAAAAC
205283 AAACAA-AAAAC
1 AAA-AACAAAAC
205294 AAAAAACAAAAC
1 -AAAAACAAAAC
205306 AAAAACAAAAC
1 AAAAACAAAAC
205317 AAA
1 AAA
205320 GAAAAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 7 0.21
11 18 0.55
12 8 0.24
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:205326 original size:11 final size:11
Alignment explanation
Indices: 205287--205343 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
205277 ACAAAAAAAC
*
205287 AAAAAACAAAA
1 AAAAAACAAAG
205298 AACAAAACAAA-
1 AA-AAAACAAAG
205309 AACAAAACAAAG
1 AA-AAAACAAAG
* *
205321 AAAAAAGAGAG
1 AAAAAACAAAG
205332 AAAAAA-AAAG
1 AAAAAACAAAG
205342 AA
1 AA
205344 CCTACTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 5 0.12
11 26 0.63
12 10 0.24
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:206430 original size:100 final size:94
Alignment explanation
Indices: 206301--206484 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
206291 CTAAACTTTC
* *
206301 TCCTTTCACTTTTCAATCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAATTGGT
1 TCCTTTCACTTTTCAATCCTCAAAGAGCAGGA------TGCCTTTCAAAGCCCACACAAATTGGT
*
206366 GGCACCTTCTAGTCCTCAAAGAGCAAGACGTTCTT
60 CGCACCTTCTAGTCCTCAAAGAGCAAGACGTTCTT
* *
206401 TCCTTTCACCTTTT-AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTCGCAC
1 TCCTTTCA-CTTTTCAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAATTGGTCGCAC
*
206465 CTTTTAGTCCTCAAAGAGCA
65 CTTCTAGTCCTCAAAGAGCA
206485 GGTGCCTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
94 47 0.61
100 25 0.32
101 5 0.06
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (94 bp):
TCCTTTCACTTTTCAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAATTGGTCGCACC
TTCTAGTCCTCAAAGAGCAAGACGTTCTT
Found at i:206624 original size:60 final size:60
Alignment explanation
Indices: 206407--207322 Score: 1021
Period size: 60 Copynumber: 15.4 Consensus size: 60
206397 TCTTTCCTTT
* * *
206407 CACCTTTTAGTCCTCAAAGAGCAGGATGC---CT--TTCAAAGCCCACACAAGTTGGTCG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * *
206462 CACCTTTTAGTCCTCAAAGAGCAGG-TGC---CT--TTCAAAGCCCATACAAGTTTGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
** * * *
206516 CATTTTTTTTAGTCCTCAAAGAGAAGGACGC---CT--TTTAAAGCCCACACAAGTTGGTGG
1 CA--CCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* ** * *
206573 CA-CTTCTCAGTCCTCAAATAATAGGACACTTTCTCCTTCAAAGCCCACACAACTTGGTGG
1 CACCTTCT-AGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * * ** * *
206633 CACCTTTTAGTCCCTCAAAGAGTAGGACACCTTTTTTTTTCAAAGCCCATACGAGTTGGTGG
1 CACCTTCTAGT-CCTCAAAGAGCAGGAC-GCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * *
206695 CACCTT-TAGTCCTCAAAGAGCAGGACACCCTTTTTCTTTTCGAAAGCCCACACGAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGG--ACGCTTTCTC-CTTC-AAAGCCCACACAAGTTGGTGG
* * * ** *
206758 CA-CTTTTAGTCCTCAAAGAGCAGGACACCTTTTTATTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGAC-GCTTTCT-CCTTCAAAGCCCACACAAGTTGGTGG
* * * **
206819 CACCTTCTGGTCCTCAAAGAGCAGGATGCCTTCTCCTTCAAAGCCCATGCAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
*
206879 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
*
206939 CACCTTCTAGTCCTCAAAGAGCAGGACG-TCTTCTCCTTCAAAG-CCACATAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCT-TTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * *
206998 CACCTTCTAGACCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGGCCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * *
207058 CACCTTCTAGTCCTCAAAAAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGAA
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTG-G
*
207119 CACCTTCTAGTCCTCAAAGAGGAGGACG-TCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCT-TTCTCCTTCAAAGCCCACACAAGTTGGTGG
*
207179 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * * * * * *
207239 CACTTTCCAATCCTCAAAGAGCAGGATGTTTTTTCCTTTTAAAGCTCACACAAGTTGGTGG
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCC-TTCAAAGCCCACACAAGTTGGTGG
207300 CACCTTCTAGTCCTCAAAGAGCA
1 CACCTTCTAGTCCTCAAAGAGCA
207323 AGACATGTTT
Statistics
Matches: 758, Mismatches: 76, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
54 31 0.04
55 42 0.06
56 20 0.03
57 27 0.04
58 2 0.00
59 55 0.07
60 315 0.42
61 154 0.20
62 72 0.09
63 40 0.05
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (60 bp):
CACCTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTCAAAGCCCACACAAGTTGGTGG
Found at i:207181 original size:121 final size:120
Alignment explanation
Indices: 206407--207322 Score: 1071
Period size: 121 Copynumber: 7.7 Consensus size: 120
206397 TCTTTCCTTT
* * *
206407 CACCTTTTAGTCCTCAAAGAGCAGGATG-C--CT--TTCAAAGCCCACACAAGTTGGTCGCACCT
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * *
206467 TTTAGTCCTCAAAGAGCAGG-TG-C--CT--TTCAAAGCCCATACAAGTTTGTGG
66 TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
** * *
206516 CATTTTTTTTAGTCCTCAAAGAGAAGGACGCC-T-T--TT-AAAGCCCACACAAGTTGGTGGCA-
1 CA--CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCAC
* ** * * *
206575 CTTCTCAGTCCTCAAATAATAGGACACTTTCTCCTTCAAAGCCCACACAACTTGGTGG
64 CTTCT-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * * ** * *
206633 CACCTTTTAGTCCCTCAAAGAGTAGGACACCTTTTTTTTTCAAAGCCCATACGAGTTGGTGGCAC
1 CACCTTCTAGT-CCTCAAAGAGCAGGACGCC-TTCTCCTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
206698 CTT-TAGTCCTCAAAGAGCAGGACACCCTTTTTCTTTTCGAAAGCCCACACGAGTTGGTGG
64 CTTCTAGTCCTCAAAGAGCAGGAC-GCC-TTCTC-CTTC-AAAGCCCACACAAGTTGGTGG
* * * ** *
206758 CA-CTTTTAGTCCTCAAAGAGCAGGACACCTTTTTATTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCC-TTCT-CCTTCAAAGCCCACACAAGTTGGTGGCAC
* * **
206822 CTTCTGGTCCTCAAAGAGCAGGATGCCTTCTCCTTCAAAGCCCATGCAAGTTGGTGG
64 CTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
206879 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
* *
206944 TCTAGTCCTCAAAGAGCAGGACGTCTTCTCCTTCAAAG-CCACATAAGTTGGTGG
66 TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* *
206998 CACCTTCTAGACCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGGCCACACAAGTTGGTGGCACCT
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
* *
207063 TCTAGTCCTCAAAAAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGAA
66 TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTG-G
* *
207119 CACCTTCTAGTCCTCAAAGAGGAGGACGTCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
207184 TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
66 TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
* * * * ** * * *
207239 CACTTTCCAATCCTCAAAGAGCAGGATGTTTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACC
1 CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCC-TTCAAAGCCCACACAAGTTGGTGGCACC
207304 TTCTAGTCCTCAAAGAGCA
65 TTCTAGTCCTCAAAGAGCA
207323 AGACATGTTT
Statistics
Matches: 703, Mismatches: 75, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
109 2 0.00
110 4 0.01
111 58 0.08
112 4 0.01
115 9 0.01
116 17 0.02
117 23 0.03
118 1 0.00
119 113 0.16
120 106 0.15
121 200 0.28
122 51 0.07
123 34 0.05
124 42 0.06
125 39 0.06
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (120 bp):
CACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGGCACCT
TCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTCAAAGCCCACACAAGTTGGTGG
Found at i:207466 original size:107 final size:107
Alignment explanation
Indices: 207249--207533 Score: 349
Period size: 107 Copynumber: 2.7 Consensus size: 107
207239 CACTTTCCAA
** * *
207249 TCCTCAAAGAGCAGGATGTTTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCTTCTAGTCCT
1 TCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCT
** *
207314 CAAAG-AGCAAGACATGTTTCATTTCCTTCTTTTCCCTTCTAG
65 CAAAGAAGCAAGACATACTTCATTTCCTTCATTTCCCTTCTAG
* * *
207356 TCCTCAAAAAGCATGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAGTCCT
1 TCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCT-TTAGTCCT
* * * * * *
207421 TAAAGAAGTAGGACCTACTTCATTTCTTTCATTTCCCTT-TTG
65 CAAAGAAGCAAGACATACTTCATTTCCTTCATTTCCCTTCTAG
* * * *
207463 TCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAGGCCCACACGAGTTGGGGGCACCTTTAGTCCT
1 TCCTCAAAGAGCAGGATGCC-TTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCT
207528 CAAAGA
65 CAAAGA
207534 GCAGGATGCC
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
107 93 0.62
108 58 0.38
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.33
Consensus pattern (107 bp):
TCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTC
AAAGAAGCAAGACATACTTCATTTCCTTCATTTCCCTTCTAG
Found at i:207594 original size:60 final size:61
Alignment explanation
Indices: 207456--207599 Score: 204
Period size: 61 Copynumber: 2.4 Consensus size: 61
207446 CTTTCATTTC
* * *
207456 CCTTTTGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAGGCCCACACGAGTTGGGGGCA
1 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCTCTTTTCAAGGCCCACACAAGTTGGGGGCA
*
207517 CCTTTAGTCCTCAAAGAGCAGGATGCC-TTCTC-TTTCGAA-GCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCTCTTTTC-AAGGCCCACACAAGTTGGGGGCA
*
207576 CCTCTTAGTCCCCAAAGAGCAGGA
1 CCT-TTAGTCCTCAAAGAGCAGGA
207600 CGTATTTCGT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
59 25 0.33
60 25 0.33
61 26 0.34
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (61 bp):
CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCTCTTTTCAAGGCCCACACAAGTTGGGGGCA
Found at i:208169 original size:20 final size:20
Alignment explanation
Indices: 208144--208217 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
208134 TTTACCTAGA
208144 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTGCAT
208164 TGTATCGATACA--TTGCTTAT
1 TGTATCGATACATTTTGC--AT
* *
208184 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTTGCAT
*
208204 TATATCGATACATT
1 TGTATCGATACATT
208218 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.09
20 40 0.85
22 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTGCAT
Found at i:209883 original size:11 final size:11
Alignment explanation
Indices: 209866--209894 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
209856 AATTCGAACG
209866 ATTTTTTTGA-
1 ATTTTTTTGAT
209876 ATTTTTTTGAT
1 ATTTTTTTGAT
209887 ATTTTTTT
1 ATTTTTTT
209895 CTCAAAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
ATTTTTTTGAT
Found at i:210569 original size:51 final size:51
Alignment explanation
Indices: 210504--210657 Score: 154
Period size: 51 Copynumber: 3.0 Consensus size: 51
210494 ATTTTTCATC
* **
210504 TCAGAGATACTCCAA-TCCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCAGGGATACTCCAACT-CCGATTTCATTTCCAAAACATCAATTTTTCGCAA
* * * **
210555 TC-GAGGATACTCCAACTCCGATTTTC-TTTCTAAAGCATCGATTTACCGCAA
1 TCAG-GGATACTCCAACTCCGA-TTTCATTTCCAAAACATCAATTTTTCGCAA
* *
210606 TCAGGGATACTCCAACTCCGATTTTATTTCCAAAACA-CTAATTTTTCACAA
1 TCAGGGATACTCCAACTCCGATTTCATTTCCAAAACATC-AATTTTTCGCAA
210657 T
1 T
210658 TGGGAAAACT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
50 5 0.06
51 71 0.87
52 6 0.07
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (51 bp):
TCAGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCGCAA
Found at i:210777 original size:28 final size:26
Alignment explanation
Indices: 210740--210811 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 26
210730 TTCATAATCG
* *
210740 GGGGGTACTCCAACGTCGTTA-TTTCA
1 GGGGATACTCCAAC-CCGTTATTTTCA
210766 TCGGGGATACTCCAATCCCGTTATTTTCGA
1 --GGGGATACTCCAA-CCCGTTATTTTC-A
210796 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
210812 CAATTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.08
28 30 0.77
29 5 0.13
30 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (26 bp):
GGGGATACTCCAACCCGTTATTTTCA
Found at i:210857 original size:51 final size:49
Alignment explanation
Indices: 210796--210963 Score: 174
Period size: 51 Copynumber: 3.3 Consensus size: 49
210786 TTATTTTCGA
** *
210796 GGGGATACTCCAACCCCAATTTTATTTCTAAAATTCCAATTTTTCACAATC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAATT--GATTTTTCACAATC
* * * * *
210847 GAGGATACTCCAACTCTGATTTTATTTCCAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCTGATTTTATTT-CTAAA-ATTGATTTTTCACAATC
* * **
210898 GGGGATACTTCAACCTTGACCTTATTTCTAAATCATTGATTTTTCACAATC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAA--ATTGATTTTTCACAATC
210949 GGGGATACTCCAACC
1 GGGGATACTCCAACC
210964 TCGTTATTTT
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 4 0.04
51 84 0.88
52 4 0.04
53 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (49 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAATTGATTTTTCACAATC
Found at i:211115 original size:79 final size:79
Alignment explanation
Indices: 210935--211117 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 79
210925 CTAAATCATT
* * * *
210935 GATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGAGAGGATACTCCAACCCTGATTTT
1 GATTTTCCATAATCGGGGATACTCCAACCTCGTTATTTCCGAGAGGATACTCCAACCCCGATTTT
* *
211000 ATTTTCAAAATATC
66 ATTTTCAAAACACC
* * ** * * * *
211014 GATTTTCTATAATCAGAAATACTCCAACCTTGTTATTTCCGAGGGGATACTCTAACCCCGGTTTT
1 GATTTTCCATAATCGGGGATACTCCAACCTCGTTATTTCCGAGAGGATACTCCAACCCCGATTTT
*
211079 A-TTTCTAGAACACC
66 ATTTTC-AAAACACC
211093 GATTTTCCATAATCGGGGATACTCC
1 GATTTTCCATAATCGGGGATACTCC
211118 GGCCCCGTTG
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 4 0.05
79 80 0.95
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (79 bp):
GATTTTCCATAATCGGGGATACTCCAACCTCGTTATTTCCGAGAGGATACTCCAACCCCGATTTT
ATTTTCAAAACACC
Found at i:212831 original size:20 final size:20
Alignment explanation
Indices: 212806--212878 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
212796 TTTTACCCAG
*
212806 ATGTATCGATACAATTTTCA
1 ATGTATCGATACAATTTTAA
* *
212826 ATGTATCGATAC-ATGTATGA
1 ATGTATCGATACAAT-TTTAA
*
212846 ATGTATCGATACATTTTTAA
1 ATGTATCGATACAATTTTAA
* *
212866 ATTTATTGATACA
1 ATGTATCGATACA
212879 TTCTGTCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.05
20 41 0.93
21 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACAATTTTAA
Found at i:219276 original size:20 final size:20
Alignment explanation
Indices: 219251--219327 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
219241 GTAAAACGAT
219251 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
*
219271 AGAATGTATCGATACATTCAC
1 AGAATGTATCGATACATT-AA
*
219292 A-CATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
* *
219311 AAAATATATCGATACAT
1 AGAATGTATCGATACAT
219328 CTAGGTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 2 0.04
20 46 0.92
21 2 0.04
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:220950 original size:32 final size:30
Alignment explanation
Indices: 220914--220972 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
220904 GAAATCAAAT
220914 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
220946 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
220973 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:221271 original size:13 final size:13
Alignment explanation
Indices: 221253--221278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
221243 ATATTTTTTG
221253 TGTATCGATACAT
1 TGTATCGATACAT
221266 TGTATCGATACAT
1 TGTATCGATACAT
221279 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:221289 original size:32 final size:33
Alignment explanation
Indices: 221232--221296 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
221222 TACAAGCCAA
221232 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
221266 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
221297 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:221290 original size:19 final size:19
Alignment explanation
Indices: 221232--221296 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
221222 TACAAGCCAA
221232 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
221253 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
221266 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
221285 TGTATCGATACA
1 TGTATCGATACA
221297 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:223839 original size:13 final size:13
Alignment explanation
Indices: 223821--223845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223811 ATAATCCCCC
223821 TGTATCGATACAG
1 TGTATCGATACAG
223834 TGTATCGATACA
1 TGTATCGATACA
223846 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:225947 original size:15 final size:15
Alignment explanation
Indices: 225927--225957 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
225917 ATTTCGTTTG
225927 GAGCTTCTTCATTTT
1 GAGCTTCTTCATTTT
*
225942 GAGCTTTTTCATTTT
1 GAGCTTCTTCATTTT
225957 G
1 G
225958 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (15 bp):
GAGCTTCTTCATTTT
Found at i:231716 original size:54 final size:52
Alignment explanation
Indices: 231601--231719 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 52
231591 AATTCTCCAC
* * * * *
231601 ATCGGGGATATTCCAACTCCGATTTATTTTCAAAACACTAATCTTTCTATAA
1 ATCGGGGATACTCAAACTCCGATTTATTTCCAAAACACCAATCTTTCGATAA
*
231653 ATCGGGGATACTCTAAACTCCGATTTATTTCCAAAAACCACCAAT-TTT-GACTCA
1 ATCGGGGATACTC-AAACTCCGATTTATTTCC-AAAA-CACCAATCTTTCGA-TAA
231707 ATCGGGGATACTC
1 ATCGGGGATACTC
231720 CACACCCCGG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
52 12 0.21
53 17 0.30
54 22 0.39
55 6 0.11
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (52 bp):
ATCGGGGATACTCAAACTCCGATTTATTTCCAAAACACCAATCTTTCGATAA
Found at i:231744 original size:29 final size:29
Alignment explanation
Indices: 231711--231785 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
231701 GACTCAATCG
231711 GGGATACTCCACACCCCGGTTA-ATCATCAA
1 GGGATACTCCA-ACCCCGGTTATATCA-CAA
*
231741 -GGATACTCCAACCCC-GTTATTTTCACAA
1 GGGATACTCCAACCCCGGTTA-TATCACAA
231769 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
231786 CTTTATTCCC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 4 0.10
28 8 0.20
29 28 0.70
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.21
Consensus pattern (29 bp):
GGGATACTCCAACCCCGGTTATATCACAA
Found at i:853800 original size:50 final size:50
Alignment explanation
Indices: 853734--853900 Score: 165
Period size: 49 Copynumber: 3.3 Consensus size: 50
853724 CGAAAATAAA
* * **
853734 GGGGTTAGAGTATCCCCGATTGTGGAAAATCGATGCTTTAGAATAAGGCC
1 GGGGTTGGAGTATCCCCGATTATGGAAAATCGATGCTTTAGAATAAAACC
* * * * *
853784 GGGGTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGGAATAAAATC
1 GGGGTTGGAGTATCCCCGATTATGGAAAATCGATGCTTTAGAATAAAACC
* * * * ** **
853833 AGAGTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATT
1 GGGGTTGGAGTATCCCCGATTATGGAAAATCGATGCTTTAG-AATAAAACC
853884 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
853901 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
49 40 0.40
50 36 0.36
51 23 0.23
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (50 bp):
GGGGTTGGAGTATCCCCGATTATGGAAAATCGATGCTTTAGAATAAAACC
Found at i:853840 original size:49 final size:51
Alignment explanation
Indices: 853787--853900 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
853777 TAAGGCCGGG
* *
853787 GTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTT-GGAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGA
** *
853836 GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATTGGG
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGA
853887 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
853901 TCGAAAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 20 0.34
50 14 0.24
51 24 0.41
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGA
Found at i:853936 original size:28 final size:30
Alignment explanation
Indices: 853887--853959 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 30
853877 TAAAATTGGG
853887 GTTGGAGTATCCCC--TCGAAAATAAT-GA
1 GTTGGAGTATCCCCGATCGAAAATAATGGA
853914 GATTGGAGTATCCCCGAT-G-AAATAATGGA
1 G-TTGGAGTATCCCCGATCGAAAATAATGGA
*
853943 GTTGGAGTACCCCCGAT
1 GTTGGAGTATCCCCGAT
853960 TATGAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 1 0.02
28 35 0.85
29 4 0.10
30 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (30 bp):
GTTGGAGTATCCCCGATCGAAAATAATGGA
Found at i:854029 original size:109 final size:108
Alignment explanation
Indices: 853834--854118 Score: 277
Period size: 109 Copynumber: 2.6 Consensus size: 108
853824 AATAAAATCA
* * * ** **
853834 GAGTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATTGGGGTTGGAGTATCC
1 GAGTTGGAGTACCCCCGATTATGAAAAAATCATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
* * *
853899 CCTCGAAAATAATGAGATTGG-AGTATCCCCGATGAAATAATG
66 CCTCGAAAATAACGAGATTGGAAGTATCCCCAATGAAATAACG
* *
853941 GAGTTGGAGTACCCCCGATTATGAAAAAAGATCATATTTTAGATATAAAGCCGGGGTTGGAGTAT
1 GAGTTGGAGTACCCCCGATTATG-AAAAA-ATCATATTTTAGAAATAAAACCGGGGTTGGAGTAT
* * *
854006 CCCCTC-AGAAATAACGGGGTTGGAAGTATCTCCAATGAAATAACG
64 CCCCTCGA-AAATAACGAGATTGGAAGTATCCCCAATGAAATAACG
* * * * * * ** * * * *
854051 GGGTTGGAGTATCACCAATTGTGAAAAATTGGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 GAGTTGGAGTACCCCCGATTATGAAAAAAT-CATATTTTAGAAATAAAACCGGGGTTGGAGTATC
854116 CCC
65 CCC
854119 GATTGCGGTA
Statistics
Matches: 144, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
107 22 0.15
108 6 0.04
109 80 0.56
110 36 0.25
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (108 bp):
GAGTTGGAGTACCCCCGATTATGAAAAAATCATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCGAAAATAACGAGATTGGAAGTATCCCCAATGAAATAACG
Found at i:854045 original size:29 final size:28
Alignment explanation
Indices: 853992--854069 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
853982 GATATAAAGC
* *
853992 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCACC-AATGAAATAA
*
854020 CGGGGTTGGAAGTATCTCCAATGAAATAA
1 CGGGGTTGG-AGTATCACCAATGAAATAA
854049 CGGGGTTGGAGTATCACCAAT
1 CGGGGTTGGAGTATCACCAAT
854070 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 21 0.47
29 24 0.53
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCACCAATGAAATAA
Found at i:856786 original size:41 final size:43
Alignment explanation
Indices: 856711--856797 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 43
856701 AAGGCAAAGG
* * *
856711 AAAAGAAAATGAAATAGGTCTTGCTCCTTGAGGACAATG-GAA
1 AAAAGAAAAGGAAATAGGTCCTGCTCCTTGAGGACAAAGTGAA
* *
856753 AAAAGAAAAGGAAA-ATGTCCTGCTTCTTGAGGACAAAGTGAA
1 AAAAGAAAAGGAAATAGGTCCTGCTCCTTGAGGACAAAGTGAA
856795 AAA
1 AAA
856798 GAGTACATCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (43 bp):
AAAAGAAAAGGAAATAGGTCCTGCTCCTTGAGGACAAAGTGAA
Found at i:856940 original size:45 final size:42
Alignment explanation
Indices: 856854--856969 Score: 128
Period size: 45 Copynumber: 2.7 Consensus size: 42
856844 ATGCTTCTTG
856854 CTCTTTGAGGACAAAAGAAAGAGGAAAATAAAGTGCATCCTA
1 CTCTTTGAGGACAAAAGAAAGAGGAAAATAAAGTGCATCCTA
* * **
856896 CTCTTTGAGGACAAAAGGGTAAAGAAGG-GAATGAAGTGTGTCCTA
1 CTCTTTGAGGACAAAA--G-AAAG-AGGAAAATAAAGTGCATCCTA
856941 CTCTTTGAGGACAAAGGAGAAA-AGGAAAA
1 CTCTTTGAGGACAAA--AGAAAGAGGAAAA
856970 AGCGTCCTGC
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
42 19 0.31
43 2 0.03
44 4 0.06
45 33 0.53
46 3 0.05
47 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (42 bp):
CTCTTTGAGGACAAAAGAAAGAGGAAAATAAAGTGCATCCTA
Found at i:856986 original size:38 final size:38
Alignment explanation
Indices: 856935--857073 Score: 127
Period size: 38 Copynumber: 3.5 Consensus size: 38
856925 AATGAAGTGT
*
856935 GTCCTACTCTTTGAGGACAAAGGAGAAAAGGAAAAAGC
1 GTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAAGC
** *
856973 GTCCTGCTCTTTGAAAACAAAAGG-GAAAAGAAAGAAATGAAATGT
1 GTCCTGCTCTTTGAGGAC-AAAGGAGAAAAG---G-AA--AAA-GC
* * *
857018 GTCATGCTCTTTGAGGATAAAGGAGAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAAGC
*
857056 ATCCTGCTCTTTGAGGAC
1 GTCCTGCTCTTTGAGGAC
857074 TAAAAAGTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
38 37 0.47
39 7 0.09
41 3 0.04
42 3 0.04
44 8 0.10
45 21 0.27
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (38 bp):
GTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAAGC
Found at i:856995 original size:83 final size:83
Alignment explanation
Indices: 856854--857069 Score: 256
Period size: 83 Copynumber: 2.6 Consensus size: 83
856844 ATGCTTCTTG
* ** *
856854 CTCTTTGAGGACAAA--AGAAAGAGGAAAATAAAGTGCATCCTACTCTTTGAGGACAAAAGGGTA
1 CTCTTTGAGGACAAAGGAGAAA-AGG--AA-AAA--GCATCCTGCTCTTTGAAAACAAAAGGGAA
* * * *
856917 AAGAAGGGAATGAAGTGTGTCCTA
60 AAGAAAGAAATGAAATGTGTCATA
*
856941 CTCTTTGAGGACAAAGGAGAAAAGGAAAAAGCGTCCTGCTCTTTGAAAACAAAAGGGAAAAGAAA
1 CTCTTTGAGGACAAAGGAGAAAAGGAAAAAGCATCCTGCTCTTTGAAAACAAAAGGGAAAAGAAA
*
857006 GAAATGAAATGTGTCATG
66 GAAATGAAATGTGTCATA
* *
857024 CTCTTTGAGGATAAAGGAGAAAAGGAAAAGGCATCCTGCTCTTTGA
1 CTCTTTGAGGACAAAGGAGAAAAGGAAAAAGCATCCTGCTCTTTGA
857070 GGACTAAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
83 86 0.75
85 3 0.03
86 2 0.02
87 15 0.13
88 3 0.03
89 5 0.04
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (83 bp):
CTCTTTGAGGACAAAGGAGAAAAGGAAAAAGCATCCTGCTCTTTGAAAACAAAAGGGAAAAGAAA
GAAATGAAATGTGTCATA
Found at i:857145 original size:61 final size:62
Alignment explanation
Indices: 857042--857348 Score: 316
Period size: 61 Copynumber: 5.1 Consensus size: 62
857032 GGATAAAGGA
* *
857042 GAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTT
1 GAAAA-GAAAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
857104 GAAAAGAAAAGGCGTCCTGCTCTTTGAGGAC-AGGAAGGTGCCACCAACTTATGTGGGCTTT
1 GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * * * **
857165 GCAAAGGGAAA-GCATACTACTCTTTGAGGACT-GGAAGGTGCCACCAACTCGAGTGATCTTT
1 G-AAAAGAAAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
857226 -AAAAGGAGAAA-GCATCCTGCTCTTTGAGGACTGGGAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAA-GA-AAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
857288 -----G-AAAGGCGTCCTGCTCTTTGAGGACTA-GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
*
857343 AAAAAG
1 GAAAAG
857349 CGTCTTGCTC
Statistics
Matches: 206, Mismatches: 27, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
55 31 0.15
56 20 0.10
57 1 0.00
59 3 0.01
60 3 0.01
61 113 0.55
62 35 0.17
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (62 bp):
GAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:857206 original size:122 final size:121
Alignment explanation
Indices: 857044--857346 Score: 359
Period size: 122 Copynumber: 2.5 Consensus size: 121
857034 ATAAAGGAGA
* *
857044 AAAGGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
1 AAAGGGAAA-GCATCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTCGTGTGGGCTTT-AAAA
* **
857109 GA-AAAGGCGTCCTGCTCTTTGAGGAC-AGGAAGGTGCCACCAACTTATGTGGGCTTTG
64 GAGAAA-GCATCCTGCTCTTTGAGGACTAGGAAAATGCCACCAACTTATGTGGGCTTTG
* * * * * **
857166 CAAAGGGAAAGCATACTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGATCTTTAAAAG
1 -AAAGGGAAAGCATCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTCGTGTGGGCTTTAAAA-
* *
857231 GAGAAAGCATCCTGCTCTTTGAGGACTGGGAAAATGCCACCAACTTGTGTGGGCTTTG
64 GAGAAAGCATCCTGCTCTTTGAGGACTAGGAAAATGCCACCAACTTATGTGGGCTTTG
* * *
857289 AAA--G---GCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAGGGAAAGCATCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTCGTGTGGGCTTTAAAA
857347 AGCGTCTTGC
Statistics
Matches: 153, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
117 44 0.29
120 1 0.01
121 4 0.03
122 66 0.43
123 38 0.25
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (121 bp):
AAAGGGAAAGCATCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGA
GAAAGCATCCTGCTCTTTGAGGACTAGGAAAATGCCACCAACTTATGTGGGCTTTG
Found at i:857422 original size:45 final size:44
Alignment explanation
Indices: 857354--857488 Score: 117
Period size: 45 Copynumber: 3.2 Consensus size: 44
857344 AAAAGCGTCT
* * *
857354 TGCTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCC
1 TGCTCTTTAAAGACAAAAGGAAAAA-AAGGGAATAAAGTGTGTCC
* *
857399 TGCTCTTTAACGAC-AAA-G-AGAAAA-GG-A-AAAG-GTGT-C
1 TGCTCTTTAAAGACAAAAGGAAAAAAAGGGAATAAAGTGTGTCC
*
857435 TCGCTCTTTAAAGACAAAAGGGAAAAAAAGGAAATGAAA-TGTGTCC
1 T-GCTCTTTAAAGACAAAA-GGAAAAAAAGGGAAT-AAAGTGTGTCC
857481 TGCTCTTT
1 TGCTCTTT
857489 GAGGATAAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
36 2 0.03
37 16 0.22
38 7 0.10
39 1 0.01
40 3 0.04
41 7 0.10
42 4 0.06
43 2 0.03
44 3 0.04
45 25 0.35
46 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (44 bp):
TGCTCTTTAAAGACAAAAGGAAAAAAAGGGAATAAAGTGTGTCC
Found at i:857434 original size:37 final size:38
Alignment explanation
Indices: 857388--857526 Score: 111
Period size: 38 Copynumber: 3.5 Consensus size: 38
857378 AGAAGGGAAT
*
857388 AAAGTGTGTCCTGCTCTTTAACGACAAA-GAGAAAAGGA
1 AAAG-GTGTCCTGCTCTTTAAAGACAAAGGAGAAAAGGA
*
857426 AAAGGTGT-CTCGCTCTTTAAAGACAAAAGGGAAAAAAAGGAAA
1 AAAGGTGTCCT-GCTCTTTAAAGAC-AAA-GG-AGAAAAGG--A
* * * *
857469 TGAAATGTGTCCTGCTCTTTGAGGATAAAGGAGAAAAGGA
1 --AAAGGTGTCCTGCTCTTTAAAGACAAAGGAGAAAAGGA
**
857509 AAAGACGTCCTGCTCTTT
1 AAAGGTGTCCTGCTCTTT
857527 GAGGACTAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
36 2 0.02
37 16 0.20
38 22 0.27
40 2 0.02
41 7 0.09
42 7 0.09
43 3 0.04
44 3 0.04
45 17 0.21
46 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (38 bp):
AAAGGTGTCCTGCTCTTTAAAGACAAAGGAGAAAAGGA
Found at i:857493 original size:459 final size:459
Alignment explanation
Indices: 856896--857804 Score: 1529
Period size: 459 Copynumber: 2.0 Consensus size: 459
856886 GTGCATCCTA
* ** * * *
856896 CTCTTTGAGGACAAAAGGGTAAAGAAGGGAATGAAGTGTGTCCTACTCTTTGAGGACAAAGGAGA
1 CTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCCTACTCTTTAACGACAAAGGAGA
856961 AAAGGAAAAAGCGTCCTGCTCTTTGAAAACAAAAGGGAAAAGAAAGAAATGAAATGTGTCATGCT
66 AAAGGAAAAAGCGTCCTGCTCTTTGAAAACAAAAGGGAAAAGAAAGAAATGAAATGTGTCATGCT
*
857026 CTTTGAGGATAAAGGAGAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAAC
131 CTTTGAGGATAAAGGAGAAAAGGAAAAGACATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAAC
* *
857091 TCGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGAGGACAGGAAGGTGCCACCAACTTAT
196 TCGTGTGGGCTTTGAAAAGAAAAGGCGACCTGCTCTTCGAGGACAGGAAGGTGCCACCAACTTAT
857156 GTGGGCTTTGCAAAGGGAAAGCATACTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGA
261 GTGGGCTTTGCAAAGGGAAAGCATACTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGA
* * *
857221 TCTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGGGAAAATGCCACCAACTTGTGTGGGCT
326 TCTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTAGCCT
*
857286 TTGAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
390 TTGAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCG
857351 TCTTG
455 TCTTG
*
857356 CTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCCTGCTCTTTAACGACAAA-GAGA
1 CTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCCTACTCTTTAACGACAAAGGAGA
* * *
857420 AAAGGAAAAGGTGT-CTCGCTCTTT-AAAGACAAAAGGGAAAA-AAAGGAAATGAAATGTGTCCT
66 AAAGGAAAAAGCGTCCT-GCTCTTTGAAA-ACAAAAGGGAAAAGAAA-GAAATGAAATGTGTCAT
*
857482 GCTCTTTGAGGATAAAGGAGAAAAGGAAAAGACGTCCTGCTCTTTGAGGACTAAAAAGTGCCACC
128 GCTCTTTGAGGATAAAGGAGAAAAGGAAAAGACATCCTGCTCTTTGAGGACTAAAAAGTGCCACC
* * *
857547 AACTCGTGTGGGCTTTGAAGAGAAAATGCGACCTGCTCTTCGAGGACTGGAAGGTGCCACCAACT
193 AACTCGTGTGGGCTTTGAAAAGAAAAGGCGACCTGCTCTTCGAGGACAGGAAGGTGCCACCAACT
* * *
857612 TATGTGGGCTTTGCAAAGGGAAAGCATCCTGCTCTTTGAGGACTGGAAGGTTCCACCAACTCGAG
258 TATGTGGGCTTTGCAAAGGGAAAGCATACTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAG
*
857677 TGGTCTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGC
323 TGATCTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGC
857742 CTTTGAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
388 CTTTGAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
857805 GGAAAAGGCG
Statistics
Matches: 421, Mismatches: 25, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
458 92 0.22
459 276 0.66
460 53 0.13
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (459 bp):
CTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCCTACTCTTTAACGACAAAGGAGA
AAAGGAAAAAGCGTCCTGCTCTTTGAAAACAAAAGGGAAAAGAAAGAAATGAAATGTGTCATGCT
CTTTGAGGATAAAGGAGAAAAGGAAAAGACATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAAC
TCGTGTGGGCTTTGAAAAGAAAAGGCGACCTGCTCTTCGAGGACAGGAAGGTGCCACCAACTTAT
GTGGGCTTTGCAAAGGGAAAGCATACTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGA
TCTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGCCTT
TGAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCGT
CTTG
Found at i:857525 original size:83 final size:81
Alignment explanation
Indices: 857344--857526 Score: 210
Period size: 82 Copynumber: 2.2 Consensus size: 81
857334 GTGGGCTTTA
* * * *
857344 AAAAGCGTCTTGCTCTTTGAGGAAAAAAGGAAAAAGAAGGGAATAAAGTGTGTCCTGCTCTTTAA
1 AAAAGCGTCCTGCTCTTTAAAGAAAAAAGGAAAAAGAAGGAAATAAAGTGTGTCCTGCTCTTTAA
857409 CGACAAAGAGAAAAGG
66 CGACAAAGAGAAAAGG
* *
857425 AAAAG-GTGTCTCGCTCTTTAAAGACAAAAGGGAAAAA-AAGGAAATGAAA-TGTGTCCTGCTCT
1 AAAAGCGT-CCT-GCTCTTTAAAGA-AAAAAGGAAAAAGAAGGAAAT-AAAGTGTGTCCTGCTCT
* * *
857487 TTGAGGATAAAGGAGAAAAGG
62 TTAACGACAAA-GAGAAAAGG
857508 AAAAGACGTCCTGCTCTTT
1 AAAAG-CGTCCTGCTCTTT
857527 GAGGACTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
80 2 0.02
81 6 0.07
82 38 0.45
83 35 0.41
84 2 0.02
85 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (81 bp):
AAAAGCGTCCTGCTCTTTAAAGAAAAAAGGAAAAAGAAGGAAATAAAGTGTGTCCTGCTCTTTAA
CGACAAAGAGAAAAGG
Found at i:857604 original size:61 final size:59
Alignment explanation
Indices: 857503--858060 Score: 545
Period size: 61 Copynumber: 9.5 Consensus size: 59
857493 ATAAAGGAGA
** *
857503 AAAGGAAAAGACGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 AAAGGAAAAG-CGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
857563 GAAGAGAAAATGCGACCTGCTCTTCGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTT
1 AAAG-GAAAA-GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * * *
857624 GCAAAGGGAAAGCATCCTGCTCTTTGAGGACTGGAAGGTTCCACCAACTCGAGTGGTCTTT
1 --AAAGGAAAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
857685 AAAAGGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGCCTTT
1 -AAAGGA-AAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
857746 ----GAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAGGAAAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
857801 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTT
1 -AAAGGAAAA-GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
857863 --A--AAAGGCGTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGAAAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
857918 ----GAAAGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAGGAAAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
857973 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTT
1 -AAAGGAAAA-GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
*
858035 --A--AAAGGCGTCCTGCTCTTTGAGGACT
1 AAAGGAAAAGCGTCCTGCTCTTTGAGGACT
858061 AATGGGCGAA
Statistics
Matches: 424, Mismatches: 54, Indels: 44
0.81 0.10 0.08
Matches are distributed among these distances:
55 125 0.29
56 41 0.10
57 6 0.01
59 2 0.00
60 16 0.04
61 176 0.42
62 55 0.13
63 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (59 bp):
AAAGGAAAAGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Done.