Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1636
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: 229876
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:146336 original size:13 final size:13
Alignment explanation
Indices: 146318--146343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146308 CAATTTTTGG
146318 TGTATCGATACAT
1 TGTATCGATACAT
146331 TGTATCGATACAT
1 TGTATCGATACAT
146344 ACTTGGTGTA
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:146355 original size:32 final size:33
Alignment explanation
Indices: 146298--146361 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
146288 TACAAGCCAA
**
146298 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
146331 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
146362 AGTTTGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:146455 original size:20 final size:20
Alignment explanation
Indices: 146402--146457 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
146392 ACATCTTTTT
*
146402 CATGTATCGATACATTGAAA
1 CATGTATCGATACTTTGAAA
*
146422 CATGTATCGATACTTTGAAT
1 CATGTATCGATACTTTGAAA
**
146442 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
146458 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGAAA
Found at i:151003 original size:15 final size:15
Alignment explanation
Indices: 150983--151013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
150973 ATTTCGTTTG
*
150983 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
150998 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
151013 G
1 G
151014 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:155100 original size:25 final size:26
Alignment explanation
Indices: 155052--155104 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
155042 CAAGCCAATG
**
155052 TATCGATACAATTTTTGGTGTATCGA
1 TATCGATACAATACTTGGTGTATCGA
155078 TATCGATAC-ATACTTGGTGTATCGA
1 TATCGATACAATACTTGGTGTATCGA
155103 TA
1 TA
155105 CAAGTTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (26 bp):
TATCGATACAATACTTGGTGTATCGA
Found at i:160153 original size:14 final size:14
Alignment explanation
Indices: 160134--160161 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
160124 GTTCCACGAG
160134 GAAGCCGGATCAAC
1 GAAGCCGGATCAAC
160148 GAAGCCGGATCAAC
1 GAAGCCGGATCAAC
160162 TCAAGTTAGC
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:0.36, C:0.29, G:0.29, T:0.07
Consensus pattern (14 bp):
GAAGCCGGATCAAC
Found at i:160867 original size:32 final size:29
Alignment explanation
Indices: 160816--160911 Score: 75
Period size: 36 Copynumber: 3.0 Consensus size: 29
160806 CCTTACAACA
*
160816 CTATCTTTCAAGGCTAAGATTGAAACCTCC
1 CTATCTTTCAAGGCTAAGATAG-AACCTCC
*
160846 CTATCTTTTCACGAGCTAAGATAGAACCTCTCTCC
1 CTATC-TTTCAAG-GCTAAGATAGAA---C-CTCC
*
160881 CTATCTTTTTCAAAGGCTAAGATAAAACCTC
1 CTATC--TTTC-AAGGCTAAGATAGAACCTC
160912 TCAATCACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
30 5 0.09
31 8 0.15
32 12 0.22
33 1 0.02
34 1 0.02
35 9 0.17
36 16 0.30
37 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (29 bp):
CTATCTTTCAAGGCTAAGATAGAACCTCC
Found at i:160874 original size:31 final size:30
Alignment explanation
Indices: 160816--160911 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 30
160806 CCTTACAACA
*
160816 CTATCTTTCAAGGCTAAGATTGAAACCTCC
1 CTATCTTTCAAGGCTAAGATAGAAACCTCC
* *
160846 CTATCTTTTCACGAGCTAAGATAGAACCTCTCTCC
1 CTATC-TTTCAAG-GCTAAGATAGAA--AC-CTCC
160881 CTATCTTTTTCAAAGGCTAAGATA-AAACCTC
1 CTATC--TTTC-AAGGCTAAGATAGAAACCTC
160912 TCAATCACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 14 0.26
33 1 0.02
34 1 0.02
35 11 0.20
36 14 0.26
37 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (30 bp):
CTATCTTTCAAGGCTAAGATAGAAACCTCC
Found at i:160887 original size:35 final size:36
Alignment explanation
Indices: 160842--160913 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
160832 AGATTGAAAC
* *
160842 CTCCCTATC-TTTTC-ACGAGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAG-GCTAAGATAAAACCTCT
160877 CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
160913 C
1 C
160914 AATCACTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 9 0.27
36 22 0.67
37 2 0.06
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
Found at i:161459 original size:13 final size:13
Alignment explanation
Indices: 161441--161465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
161431 TGCCAGTTTT
161441 ATGTATCGATACA
1 ATGTATCGATACA
161454 ATGTATCGATAC
1 ATGTATCGATAC
161466 TAAGCAAAAT
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):
ATGTATCGATACA
Found at i:176909 original size:13 final size:13
Alignment explanation
Indices: 176891--176916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
176881 TACACCAAGT
176891 ATGTATCGATACA
1 ATGTATCGATACA
176904 ATGTATCGATACA
1 ATGTATCGATACA
176917 CCAAAAATTG
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:176914 original size:32 final size:33
Alignment explanation
Indices: 176873--176936 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
176863 TAGCCAAACT
**
176873 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
176905 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
176937 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:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:178562 original size:21 final size:21
Alignment explanation
Indices: 178536--178577 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
178526 AATCAACCAT
* *
178536 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
178557 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
178578 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:182496 original size:13 final size:13
Alignment explanation
Indices: 182478--182503 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
182468 TACACCAAGT
182478 ATGTATCGATACA
1 ATGTATCGATACA
182491 ATGTATCGATACA
1 ATGTATCGATACA
182504 CCAAAAATTG
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:182501 original size:32 final size:33
Alignment explanation
Indices: 182460--182523 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
182450 TAGCCAAACT
**
182460 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
182492 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
182524 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:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:185928 original size:19 final size:19
Alignment explanation
Indices: 185900--185968 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
185890 TTTTTACCCA
185900 GATGTATCGATATATTTTC
1 GATGTATCGATATATTTTC
* *
185919 GATCTATCGATATATTTTT
1 GATGTATCGATATATTTTC
*
185938 GATGTATCCATATATTTTC
1 GATGTATCGATATATTTTC
185957 GATGTATCGATA
1 GATGTATCGATA
185969 CATGTATGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (19 bp):
GATGTATCGATATATTTTC
Found at i:185942 original size:38 final size:38
Alignment explanation
Indices: 185900--185988 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
185890 TTTTTACCCA
* * *
185900 GATGTATCGATATATTTTCGATCTATCGATATATTTTT
1 GATGTATCGATATATTTTCGATCTATCGATACATGTAT
* *
185938 GATGTATCCATATATTTTCGATGTATCGATACATGTAT
1 GATGTATCGATATATTTTCGATCTATCGATACATGTAT
185976 GAATGTATCGATA
1 G-ATGTATCGATA
185989 CATTCTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 34 0.77
39 10 0.23
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (38 bp):
GATGTATCGATATATTTTCGATCTATCGATACATGTAT
Found at i:187481 original size:13 final size:13
Alignment explanation
Indices: 187441--187482 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
187431 CGTTTAAGGT
187441 AATGTATTGATAC
1 AATGTATTGATAC
*
187454 -ATGATTATCGATAC
1 AATG--TATTGATAC
187468 AATGTATTGATAC
1 AATGTATTGATAC
187481 AA
1 AA
187483 GGTGCCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 8 0.33
15 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (13 bp):
AATGTATTGATAC
Found at i:190135 original size:97 final size:96
Alignment explanation
Indices: 190012--190251 Score: 381
Period size: 97 Copynumber: 2.5 Consensus size: 96
190002 TTGAAAAATG
* * *
190012 GGGTTGGAGTATCCTCTCGGATGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGA
1 GGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGA
*
190077 ATAAAATTTGAACTTTGATGCGTTTAAAAGC
66 ATAAAATTTAAACTTTGATGCGTTTAAAAGC
190108 AGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAG
1 -GGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAG
* *
190173 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
65 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
* * *
190205 GAGATTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTATCCCCGAT
1 G-GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGAT
190252 AAATAAAATT
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
96 1 0.01
97 132 0.99
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (96 bp):
GGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGA
ATAAAATTTAAACTTTGATGCGTTTAAAAGC
Found at i:192481 original size:20 final size:20
Alignment explanation
Indices: 192458--192523 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
192448 GAATGTATGG
192458 ATACATTGAAAAAAGTATCA
1 ATACATTGAAAAAAGTATCA
* * * *
192478 ATACATTCATACATA-TATCG
1 ATACATTGA-AAAAAGTATCA
*
192498 ATACATTGACAAAAGTATCA
1 ATACATTGAAAAAAGTATCA
192518 ATACAT
1 ATACAT
192524 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.86
21 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (20 bp):
ATACATTGAAAAAAGTATCA
Found at i:193326 original size:48 final size:48
Alignment explanation
Indices: 193202--193333 Score: 201
Period size: 48 Copynumber: 2.8 Consensus size: 48
193192 AGAGGAGTGC
** ** **
193202 CAATGTGCCAATTCAAGGCCAATGACATCAAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
*
193250 CAATGTGCTGATTCAAGGCCAGCGACATTGAGTTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
193298 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA
193334 TAAAGGTGCC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
Found at i:193488 original size:28 final size:29
Alignment explanation
Indices: 193444--193668 Score: 230
Period size: 28 Copynumber: 7.8 Consensus size: 29
193434 AAAATAAAGG
193444 TGCCACTAACTTATGTGGGCTTT-AAAGAGA
1 TGCCACTAAC-T-TGTGGGCTTTGAAAGAGA
*
193474 TGCCACTAACTTGTGGG-TTTGAAAAGATGC
1 TGCCACTAACTTGTGGGCTTTG-AAAGA-GA
* *
193504 TGCCACTAACTCGTGGGCTTTGGAAG-GA
1 TGCCACTAACTTGTGGGCTTTGAAAGAGA
** *
193532 TGCCACTAACTCATGGGCTTTGAAA-AGG
1 TGCCACTAACTTGTGGGCTTTGAAAGAGA
* * *
193560 TGCCATTGACTTGTGGGCTTGGAAA-AGA
1 TGCCACTAACTTGTGGGCTTTGAAAGAGA
* *
193588 TGCCATTGACTTGTGGGCTTTGAAA-AGA
1 TGCCACTAACTTGTGGGCTTTGAAAGAGA
* *
193616 TGCCACTGACTTGTGGTCTTTTG-AAGAGA
1 TGCCACTAACTTGTGGGC-TTTGAAAGAGA
*
193645 TGCCACTAACTTGTGGACTTTGAA
1 TGCCACTAACTTGTGGGCTTTGAA
193669 GAGGTCACAA
Statistics
Matches: 169, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
27 3 0.02
28 102 0.60
29 30 0.18
30 30 0.18
31 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (29 bp):
TGCCACTAACTTGTGGGCTTTGAAAGAGA
Found at i:199927 original size:97 final size:97
Alignment explanation
Indices: 199799--200036 Score: 305
Period size: 97 Copynumber: 2.5 Consensus size: 97
199789 TTTTTTATTG
* * * *
199799 AAAAACGGGGTTAGAGTATCTCCTCGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTA
* * *
199864 AGTGAGAATAAAATTTGAACTTTGATGCATTT
66 AGTAAGAATAAAATTTAAACTTTGATACATTT
* * * *
199896 AAAAGCGGGGTTGGAGTCTCCCCTCGAAGGAATGGGGTTGAAGTGTCCCCGATGGTGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTA
* * **
199961 AGTAAGAATCAGATTTAAACTTTGATATGTTT
66 AGTAAGAATAAAATTTAAACTTTGATACATTT
* * * *
199993 AAAAGCGAGATTGGAGTATCCCCTCGGAGGAATAGGGTTAGAGT
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGT
200037 ATTCCTGATA
Statistics
Matches: 119, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 119 1.00
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (97 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTA
AGTAAGAATAAAATTTAAACTTTGATACATTT
Found at i:202208 original size:20 final size:20
Alignment explanation
Indices: 202179--202347 Score: 99
Period size: 20 Copynumber: 7.8 Consensus size: 20
202169 AAAAAAAGAT
*
202179 AGAATATATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
202199 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
202219 TA-CATGTCTCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
202239 AAAATGTATCCATACATCTAGGTAAAAAAAA
1 AGAATGTATCGATACAT-T--G--------A
*
202270 TAGAATGTTTCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
202291 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
202311 TA-CATGAATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
202331 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
202348 ACTTTTTCAT
Statistics
Matches: 115, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.02
20 91 0.79
21 4 0.03
23 1 0.01
29 1 0.01
31 2 0.02
32 14 0.12
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:202215 original size:52 final size:50
Alignment explanation
Indices: 202151--202307 Score: 145
Period size: 52 Copynumber: 3.3 Consensus size: 50
202141 CATTTTTCAT
*
202151 TGTATCGATACATCTGGAAAAAAAAGATAGAATATATCGATACATTGAAGAA
1 TGTATCGATACATCTGG-AAAAAAA-ATAGAATGTATCGATACATTGAAGAA
* * * *
202203 TGTATCGATACAT-T--------CATA-CATGTCTCGATACATTGAAAAA
1 TGTATCGATACATCTGGAAAAAAAATAGAATGTATCGATACATTGAAGAA
* *
202243 TGTATCCATACATCTAGGTAAAAAAAATAGAATGTTTCGATACATTGAAGAA
1 TGTATCGATACATCT-GG-AAAAAAAATAGAATGTATCGATACATTGAAGAA
202295 TGTATCGATACAT
1 TGTATCGATACAT
202308 TCATACATGA
Statistics
Matches: 82, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
40 30 0.37
41 4 0.05
51 4 0.05
52 44 0.54
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (50 bp):
TGTATCGATACATCTGGAAAAAAAATAGAATGTATCGATACATTGAAGAA
Found at i:202294 original size:92 final size:92
Alignment explanation
Indices: 202151--202347 Score: 324
Period size: 92 Copynumber: 2.1 Consensus size: 92
202141 CATTTTTCAT
202151 TGTATCGATACATCTGGAAAAAAAAGATAGAATATATCGATACATTGAAGAATGTATCGATACAT
1 TGTATCGATACATCTGGAAAAAAAAGATAGAATATATCGATACATTGAAGAATGTATCGATACAT
**
202216 TCATACATGTCTCGATACATTGAAAAA
66 TCATACATGAATCGATACATTGAAAAA
* * * *
202243 TGTATCCATACATCTAGGTAAAAAAA-ATAGAATGTTTCGATACATTGAAGAATGTATCGATACA
1 TGTATCGATACATCT-GGAAAAAAAAGATAGAATATATCGATACATTGAAGAATGTATCGATACA
202307 TTCATACATGAATCGATACATTGAAAAA
65 TTCATACATGAATCGATACATTGAAAAA
202335 TGTATCGATACAT
1 TGTATCGATACAT
202348 ACTTTTTCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
92 88 0.91
93 9 0.09
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (92 bp):
TGTATCGATACATCTGGAAAAAAAAGATAGAATATATCGATACATTGAAGAATGTATCGATACAT
TCATACATGAATCGATACATTGAAAAA
Found at i:208241 original size:15 final size:15
Alignment explanation
Indices: 208223--208257 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
208213 CGAGTCAACT
208223 TCATCATTATCATCA
1 TCATCATTATCATCA
*
208238 TCATCATTATCTTCA
1 TCATCATTATCATCA
208253 TCATC
1 TCATC
208258 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:210549 original size:14 final size:14
Alignment explanation
Indices: 210530--210561 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
210520 ATCACTATTC
*
210530 ATCACTGTTCATGT
1 ATCACTATTCATGT
210544 ATCACTATTCATGT
1 ATCACTATTCATGT
210558 ATCA
1 ATCA
210562 ATACATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (14 bp):
ATCACTATTCATGT
Found at i:210573 original size:13 final size:13
Alignment explanation
Indices: 210555--210594 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
210545 TCACTATTCA
*
210555 TGTATCAATACAT
1 TGTATCGATACAT
*
210568 TGTATCGATACAG
1 TGTATCGATACAT
210581 TGTATCGATACAT
1 TGTATCGATACAT
210594 T
1 T
210595 ATGAATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:210686 original size:20 final size:19
Alignment explanation
Indices: 210642--210679 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
210632 TTTCAAATGT
*
210642 ATGTATCGATACATTATGA
1 ATGTATCGATACATTAGGA
210661 ATTGTATCGATACA-TAGGA
1 A-TGTATCGATACATTAGGA
210680 GCATGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTAGGA
Found at i:213153 original size:27 final size:27
Alignment explanation
Indices: 213123--213194 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
213113 TTGTCATTGG
*
213123 GGATACTCTAACCCCATTCCTTCAAAA
1 GGATACTCCAACCCCATTCCTTCAAAA
213150 GGATACTCCAACCCCATTCCTTCAAAA
1 GGATACTCCAACCCCATTCCTTCAAAA
213177 GGATACTCCAACCCCATT
1 GGATACTCCAACCCCATT
213195 TTTTAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (27 bp):
GGATACTCCAACCCCATTCCTTCAAAA
Found at i:215029 original size:167 final size:166
Alignment explanation
Indices: 214828--215151 Score: 510
Period size: 167 Copynumber: 1.9 Consensus size: 166
214818 ATGGGATCGG
214828 AAACTCAATTTTTCAAAAAAAAGGCATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATTA
1 AAACTCAATTTTTCAAAAAAAAGGCATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATTA
* * * * *
214893 ATTTTTTAAACTTGATTTAATATGAGTTAAATGCTGATATTTTATGAATTTTAAAAATAAAAAAC
66 ATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAAAC
214958 CAAGAAA-AATCC-CCC-AAAACAATTTATGAAATAGA
131 CAA-AAAGAATCCTCCCGAAAA-AATTTATGAAATAGA
* *
214993 AAACTCGATTTTTCGAAAAAAAAGGGCATTTCAAAGAAAAAAATCCAAAACTTATGAAAATGAAT
1 AAACTCAATTTTTC-AAAAAAAA-GGCATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAAT
*
215058 TAATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATCAAAA
64 TAATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAA
*
215123 ATCAAAAAGAATCCTCCCGAAAAAATTTA
129 ACCAAAAAGAATCCTCCCGAAAAAATTTA
215152 CAAAGTAAAA
Statistics
Matches: 145, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 13 0.09
166 11 0.08
167 108 0.74
168 9 0.06
169 4 0.03
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (166 bp):
AAACTCAATTTTTCAAAAAAAAGGCATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATTA
ATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAAAC
CAAAAAGAATCCTCCCGAAAAAATTTATGAAATAGA
Found at i:215193 original size:167 final size:166
Alignment explanation
Indices: 214828--215193 Score: 463
Period size: 167 Copynumber: 2.2 Consensus size: 166
214818 ATGGGATCGG
* * *
214828 AAACTCAATTTTTCAAAAAAAAG-GCATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATT
1 AAACTCCATATTTCAAAAAAAAGAGAATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATT
* * * * *
214892 AATTTTTTAAACTTGATTTAATATGAGTTAAATGCTGATATTTTATGAATTTTAAAAATAAAAAA
66 AATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAAA
* *
214957 CCAAGAAAAATCCCCCAAAACAATTTATGAAATAGA
131 CCAAGAAAAATCCCCCAAAACAATTTATCAAATAAA
* * * * *
214993 AAACTCGATTTTTCGAAAAAAAAGGGCATTTCAAAGAAAAAAATCCAAAACTTATGAAAATGAAT
1 AAACTCCATATTTC-AAAAAAAAGAGAATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAAT
*
215058 TAATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATCAAAA
65 TAATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAA
*
215123 ATCAA-AAAGAATCCTCCCGAAAA-AATTTA-CAAAGTAAA
130 ACCAAGAAA-AATCC-CCC-AAAACAATTTATCAAA-TAAA
* **
215161 AAACTCCATAATTT-AGAAACGAGAGAATTTCAA
1 AAACTCCAT-ATTTCAAAAAAAAGAGAATTTCAA
215194 TGTGGTCAAA
Statistics
Matches: 176, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
165 13 0.07
166 12 0.07
167 124 0.70
168 20 0.11
169 7 0.04
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (166 bp):
AAACTCCATATTTCAAAAAAAAGAGAATTTCAAAGAAAAAAATCCAAAAATTATGAAAATGAATT
AATTTTTTAAAATTAATTTAATATAAGTTAAATGATGATATTTGATGAATTTTAAAAATAAAAAA
CCAAGAAAAATCCCCCAAAACAATTTATCAAATAAA
Found at i:215339 original size:47 final size:46
Alignment explanation
Indices: 215208--216103 Score: 624
Period size: 47 Copynumber: 19.0 Consensus size: 46
215198 GTCAAATGAT
* *
215208 GGTG-GAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAACAA
1 GGTGAGAAA-AGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* *
215254 GGT-AAAAAGAGTTTGACCT-GGTCCTAATGCCAATACAGTCAAATAA
1 GGTGAGAAA-AGTTTGA-CTAGGTCCTAATGCCAATACAGTCAAACAA
* * * *
215300 TGGTGAGAAAAGTGTGACTAGGTTCTAACGCTAATACAGTCAAACAA
1 -GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* *
215347 GG-GTA-AAAAGTGTTTGACTAAGTCCTAATGCCAATATAGTCAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
** * *
215394 GG-GTA-AAAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * ** *
215441 GGTGACAAGAGTTTGACCAAATCCTAATGCCAATATAGTCAAACAA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * *
215487 GAGTG-GAAAGAGTTTGACTAGATCCTACA-GCCAATATAGTCAAATGAT
1 G-GTGAGAAA-AGTTTGACTAGGTCCTA-ATGCCAATACAGTCAAA-CAA
* * * * *
215535 GGT-AGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAA
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * * *
215583 GGGTGAGAAAAGTTTGACTAGGTTCTAACGCCAATATAATCAAACGA
1 -GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * *
215630 GG-GTA-AAAATTGTTTGATTAGGTCCTAATGCCAATATAGTTAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * ***
215677 GGTGAGAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * *
215723 GAGT-AGAAGGAGTTTGACTTGGTCCTAATGCCAATACAGTCAAACGAT
1 G-GTGAGAA-AAGTTTGACTAGGTCCTAATGCCAATACAGTCAAAC-AA
* *
215771 GGTG-GAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGAT
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATACAGTCAAAC-AA
* * * *
215820 GGTG-GAATTTAAGTTTGACCAGGTCCTAACGCCAATACAGTTAAATAA
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * * * **
215868 GGGTAAGAAAAGTTTGACCAGGTTCTAATGTCAATATAGTCAAATGA
1 -GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * *
215915 GG-GTA-AAAAGTGTTTGACTAGGTCCCAATGCTAATACAGTTAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* * * * **
215962 GGTGAGAAGAGTTTGACCATGTCCTAACGCCAATTTAGTCAAACAA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
* *
216008 GAGTG-GAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTCAAACGAT
1 G-GTGAGAAA-AGTTTGACTAGGTCCTAATGCCAATACAGTCAAAC-AA
** * *
216056 GGTG-GTATTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAA
1 GGTGAG-A--AAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
216104 TCATGAAATT
Statistics
Matches: 688, Mismatches: 117, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
45 14 0.02
46 147 0.21
47 346 0.50
48 27 0.04
49 147 0.21
50 7 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (46 bp):
GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA
Found at i:215484 original size:93 final size:93
Alignment explanation
Indices: 215213--216103 Score: 675
Period size: 93 Copynumber: 9.4 Consensus size: 93
215203 ATGATGGTGG
* * * *
215213 AAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAACAAGGTAAAAAGAGTTTGACCT-GGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAAGGTAAAAAGAGTTTGA-CTAGGTC
* * * *
215277 CTAATGCCAATACAGTCAAATAATGGTGAG
65 CTAATGCCAATATAGTCAAACAAGGGT-AA
* * * * * *
215307 AAA-AGTGTGACTAGGTTCTAACGCTAATACAGTCAAACAAGGGTAAAAAGTGTTTGACTAAGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAA-GGTAAAAAGAGTTTGACTAGGTC
215371 CTAATGCCAATATAGTCAAACAAGGGTAA
65 CTAATGCCAATATAGTCAAACAAGGGTAA
* * * * * * **
215400 AAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGACAAGAGTTTGACCAAATCC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAAGGTAAAAAGAGTTTGACTAGGTCC
* **
215465 TAATGCCAATATAGTCAAACAAGAGTGG
66 TAATGCCAATATAGTCAAACAAGGGTAA
* * * **
215493 AAAGAGTTTGACTAGATCCT-ACAGCCAATATAGTCAAATGATGGTAGAATTTGAGTTTGACTAG
1 AAAGAGTTTGACTAGGTCCTAAC-GCCAATATAGTCAAA-CAAGGTA-AA-AAGAGTTTGACTAG
* * * * *
215557 ATCCAAATGCCAATAAAGTCAAATAAGGGTGAG
62 GTCCTAATGCCAATATAGTCAAACAAGGGT-AA
* * * ** *
215590 AAA-AGTTTGACTAGGTTCTAACGCCAATATAATCAAACGAGGGTAAAAATTGTTTGATTAGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAAC-AAGGTAAAAAGAGTTTGACTAGGTC
* *
215654 CTAATGCCAATATAGTTAAACAA-GGTGA
65 CTAATGCCAATATAGTCAAACAAGGGTAA
* * * *** * * *
215682 GAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGAGAGTAGAAGGAGTTTGACTTGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAAG-GTAAAAAGAGTTTGACTAGGTC
* * *
215747 CTAATGCCAATACAGTCAAACGATGGTGGAA
65 CTAATGCCAATATAGTCAAAC-AAGG-GTAA
*** * * * ** *
215778 TTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGAATTTA-AGTTTGACCAG
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAAC-AAGGT--AA-AAAGAGTTTGACTAG
* * * *
215842 GTCCTAACGCCAATACAGTTAAATAAGGGTAA
62 GTCCTAATGCCAATATAGTCAAACAAGGGTAA
* * * * * * *
215874 GAAA-AGTTTGACCAGGTTCTAATGTCAATATAGTCAAATGAGGGTAAAAAGTGTTTGACTAGGT
1 -AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAA-CAAGGTAAAAAGAGTTTGACTAGGT
* * * * *
215938 CCCAATGCTAATACAGTTAAACAA-GGTGA
64 CCTAATGCCAATATAGTCAAACAAGGGTAA
* * * * **
215967 GAAGAGTTTGACCATGTCCTAACGCCAATTTAGTCAAACAAGAGTGGAAAGAGTTTGACTAGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAAG-GTAAAAAGAGTTTGACTAGGTC
* * *
216032 TTAATGCCAATACAGTCAAACGATGGTGGT-A
65 CTAATGCCAATATAGTCAAAC-A-AG-GGTAA
*** * *
216063 TTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAA
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAA
216104 TCATGAAATT
Statistics
Matches: 628, Mismatches: 141, Indels: 54
0.76 0.17 0.07
Matches are distributed among these distances:
92 9 0.01
93 249 0.40
94 144 0.23
95 4 0.01
96 178 0.28
97 13 0.02
98 31 0.05
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (93 bp):
AAAGAGTTTGACTAGGTCCTAACGCCAATATAGTCAAACAAGGTAAAAAGAGTTTGACTAGGTCC
TAATGCCAATATAGTCAAACAAGGGTAA
Found at i:215635 original size:236 final size:235
Alignment explanation
Indices: 215214--216103 Score: 804
Period size: 236 Copynumber: 3.8 Consensus size: 235
215204 TGATGGTGGA
* * * *
215214 AAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAACAAG-GTAAAAAGAGTTTGACCTGGTCC
1 AAGAGTTTGACTAGATCCTAATGCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGA-CTGGTCC
* * * * * *
215278 TAATGCCAATACAGTCAAATAATGGTGAGAA---AAGTGTGACTAGGTTCTAACGCTAATACAGT
65 TAATGCCAATACAGTCAAATGATGGT-AGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGT
* * *
215340 CAAACAAGGGT-A-AAAAGTGTTTGACTAAGTCCTAATGCCAATATAGTCAAACAAGGGTAAAAA
129 CAAACAAGGGTGAGAAAA--GTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGGTAAAAA
215403 GTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGAC
192 GTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGAC
* * * * *
215447 AAGAGTTTGACCAAATCCTAATGCCAATATAGTCAAACAAGAGTGGAAAGAGTTTGACTAGATCC
1 AAGAGTTTGACTAGATCCTAATGCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGACT-GGTCC
* * * *
215512 TACA-GCCAATATAGTCAAATGATGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGT
65 TA-ATGCCAATACAGTCAAATGATGGTAGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGT
* * * *
215576 CAAATAAGGGTGAGAAAAGTTTGACTAGGTTCTAACGCCAATATAATCAAACGAGGGTAAAAATT
129 CAAACAAGGGTGAGAAAAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGGTAAAAAGT
* ** * * *
215641 GTTTGATTAGGTCCTAATGCCAATATAGTTAAACAAGGTGAG
194 GTTTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGAC
* *** *
215683 AAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGAGAGTAGAAGGAGTTTGACTTGGTCC
1 AAGAGTTTGACTAGATCCTAATGCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGAC-TGGTCC
* *
215748 TAATGCCAATACAGTCAAACGATGGTGGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTC
65 TAATGCCAATACAGTCAAATGATGGTAGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTC
* * * * * * *
215813 AAACGATGGTG-GAATTTAAGTTTGACCAGGTCCTAACGCCAATACAGTTAAATAAGGGTAAGAA
130 AAACAAGGGTGAGAA---AAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGGTAA-AA
* * * *** * * * * *
215877 A-AGTTTGACCAGGTTCTAATGTCAATATAGTCAAATGAGGGTAAA
191 AGTGTTTGACTAGGTCCTAACACCAATATAATCAAA-CAAGGTGAC
* * * * *
215922 AAGTGTTTGACTAGGTCCCAATGCTAATACAGTTAAACAAG-GT-GAGAAGAGTTTGACCAT-GT
1 AAGAGTTTGACTAGATCCTAATGCCAATACAGTCAAACAAGAGTAGA-AAGAGTTTGA-C-TGGT
* ** * * * * *
215984 CCTAACGCCAATTTAGTCAAA-CAAGAGTGGAA--AGAGTTTGACTAGGTCTTAATGCCAATACA
63 CCTAATGCCAATACAGTCAAATGATG-GTAGAATTTGAGTTTGACTAGGTCCTAATGCCAATACA
* * ** * * *
216046 GTCAAACGATGGTG-GTATTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAA
127 GTCAAACAAGGGTGAG-A--AAAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAA
216104 TCATGAAATT
Statistics
Matches: 544, Mismatches: 92, Indels: 39
0.81 0.14 0.06
Matches are distributed among these distances:
233 41 0.08
234 39 0.07
235 5 0.01
236 304 0.56
237 7 0.01
238 106 0.19
239 42 0.08
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (235 bp):
AAGAGTTTGACTAGATCCTAATGCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGACTGGTCCT
AATGCCAATACAGTCAAATGATGGTAGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCA
AACAAGGGTGAGAAAAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGGTAAAAAGTGT
TTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGAC
Found at i:215905 original size:285 final size:280
Alignment explanation
Indices: 215198--216172 Score: 1113
Period size: 285 Copynumber: 3.5 Consensus size: 280
215188 TTTCAATGTG
* * * *
215198 GTCAAATGATGGTGGAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAAC-AAGGT--AA-
1 GTCAAACGATGGTGGAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGAAT
** * * * * * *
215259 AAAGAGTTTGACCTGGTCCTAATGCCAATACAGTCAAATAATGGTGAGAAAAGTGTGACTAGGTT
66 TTA-AGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGACCAGGTT
* * * *
215324 CTAACGCTAATACAGTCAAACAAGGGTAAAAAGTGTTTGACTAAGTCCTAATGCCAATATAGTCA
130 CTAACGC-AATATAGTCAAACGAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAATATAGTTA
* * * * *
215389 AACAAGGGTAAAAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAG-GTGACAAGAGT
194 AACAA-GGTGAGAAGAGTTTGACTA-GTCCTAACGCCAATATAGTCAAACAAGAGTGA-AAGAGT
* ** *
215453 TTGACCAAATCCTAATGCCAATATA
256 TTGACTAGGTCCTAATGCCAATACA
* * * * *
215478 GTCAAAC-AAGAGTGGAAAGAGTTTGACTAGATCCTACA-GCCAATATAGTCAAATGATGGTAGA
1 GTCAAACGATG-GTGGAAAGAGTTTGACTAGGTCCTA-ATGCCAATACAGTCAAACGATGGTGGA
* * * * * *
215541 ATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAAGGGTGAGAAAAGTTTGACTAGGT
64 ATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGACCAGGT
* * *
215606 TCTAACGCCAATATAATCAAACGAGGGTAAAAATTGTTTGATTAGGTCCTAATGCCAATATAGTT
129 TCTAACG-CAATATAGTCAAACGAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAATATAGTT
* *** *
215671 AAACAAGGTGAGAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGAGAGTAGAAGGAGT
193 AAACAAGGTGAGAAGAGTTTGACTAG-TCCTAACGCCAATATAGTCAAACAAGAGT-GAAAGAGT
*
215736 TTGACTTGGTCCTAATGCCAATACA
256 TTGACTAGGTCCTAATGCCAATACA
*
215761 GTCAAACGATGGTGGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGA
1 GTCAAACGATGGTGGAA--AGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGA
* * *
215826 ATTTAAGTTTGACCAGGTCCTAACGCCAATACAGTTAAATAAGGGTAAGAAAAGTTTGACCAGGT
64 ATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGACCAGGT
* * * * *
215891 TCTAATGTCAATATAGTCAAATGAGGGTAAAAAGTGTTTGACTAGGTCCCAATGCTAATACAGTT
129 TCTAACG-CAATATAGTCAAACGAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAATATAGTT
* *
215956 AAACAAGGTGAGAAGAGTTTGACCATGTCCTAACGCCAATTTAGTCAAACAAGAGTGGAAAGAGT
193 AAACAAGGTGAGAAGAGTTTGACTA-GTCCTAACGCCAATATAGTCAAACAAGAGT-GAAAGAGT
*
216021 TTGACTAGGTCTTAATGCCAATACA
256 TTGACTAGGTCCTAATGCCAATACA
** * * * ** *
216046 GTCAAACGATGGTGGTATTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAATCATGAA
1 GTCAAACGATGGTGG-A-AAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGA
* * *
216111 ATTTGAGTTTGACCA-ATCCTAATGCCAATACAATTAAATAAGGGTGAA-AAAAGTTTGACCAG
64 ATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGT-AAGAAAAGTTTGACCAG
216173 ATATAGTGAA
Statistics
Matches: 592, Mismatches: 85, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
279 2 0.00
280 42 0.07
281 6 0.01
282 36 0.06
283 157 0.27
284 47 0.08
285 300 0.51
286 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (280 bp):
GTCAAACGATGGTGGAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGAAT
TTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGACCAGGTTC
TAACGCAATATAGTCAAACGAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAATATAGTTAAA
CAAGGTGAGAAGAGTTTGACTAGTCCTAACGCCAATATAGTCAAACAAGAGTGAAAGAGTTTGAC
TAGGTCCTAATGCCAATACA
Found at i:216159 original size:48 final size:49
Alignment explanation
Indices: 216017--216144 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 49
216007 AGAGTGGAAA
* * * * * * **
216017 GAGTTTGACTAGGTCTTAATGCCAATACAGTCAAACGATG-GTGGTATTT
1 GAGTTTGACCAGATCCTAATGCCAATACAATCAAAC-AAGCATGAAATTT
* * * *
216066 GAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAATCATGAAATTT
1 GAGTTTGACCAGATCCTAATGCCAATACAATCAAACAAGCATGAAATTT
216115 GAGTTTGACCA-ATCCTAATGCCAATACAAT
1 GAGTTTGACCAGATCCTAATGCCAATACAAT
216145 TAAATAAGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
48 17 0.25
49 50 0.75
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (49 bp):
GAGTTTGACCAGATCCTAATGCCAATACAATCAAACAAGCATGAAATTT
Found at i:218134 original size:20 final size:20
Alignment explanation
Indices: 218088--218148 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
218078 CAACACCTTT
* **
218088 TTCAATGTATCGATATATGG
1 TTCAATGTATCGATACATTC
* *
218108 ATGAATGTATCGATACATTC
1 TTCAATGTATCGATACATTC
218128 TTCAATGTATCGATACATTC
1 TTCAATGTATCGATACATTC
218148 T
1 T
218149 ACCCTGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TTCAATGTATCGATACATTC
Found at i:218162 original size:23 final size:20
Alignment explanation
Indices: 218111--218168 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
218101 TATATGGATG
*
218111 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTCC
218131 AATGTATCGATACATTCTACCC
1 AATGTATCGATACATTCT--CC
*
218153 TGATGTATCGATACAT
1 -AATGTATCGATACAT
218169 CTAGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCTCC
Found at i:229793 original size:20 final size:20
Alignment explanation
Indices: 229730--229803 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
229720 TTTTAACTAG
*
229730 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAAAA
* * * * *
229750 ATGAATTGATAAATTCAAAC
1 ATGTATCGATACATTGAAAA
229770 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
229790 ATGTATCGATACAT
1 ATGTATCGATACAT
229804 ATGGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Done.