Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000142.1 Hibiscus syriacus cultivar Beakdansim tig00000257_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 196534
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:3559 original size:9 final size:8
Alignment explanation
Indices: 3541--3592 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
3531 TTTTACGCTT
3541 AAAAAAGA
1 AAAAAAGA
3549 AAAACAAG-
1 AAAA-AAGA
3557 AAAAAAGA
1 AAAAAAGA
3565 AAAAAA-A
1 AAAAAAGA
*
3572 AAAAGAGA
1 AAAAAAGA
3580 AAATGAAAGA
1 AAA--AAAGA
3590 AAA
1 AAA
3593 TATGGGTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 9 0.24
8 18 0.49
9 3 0.08
10 7 0.19
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:3577 original size:20 final size:22
Alignment explanation
Indices: 3542--3592 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3532 TTTACGCTTA
3542 AAAAAGAAAAACAAGA-AAAAAG
1 AAAAA-AAAAACAAGAGAAAAAG
*
3564 AAAAAAAAAA-AAGAGAAAATG
1 AAAAAAAAAACAAGAGAAAAAG
*
3585 AAAGAAAA
1 AAAAAAAA
3593 TATGGGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAACAAGAGAAAAAG
Found at i:3592 original size:22 final size:21
Alignment explanation
Indices: 3544--3592 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3534 TACGCTTAAA
*
3544 AAAG-AAAAACAAGAAAAAAG
1 AAAGAAAAAAAAAGAAAAAAG
*
3564 AAA-AAAAAAAAAGAGAAAATG
1 AAAGAAAAAAAAAGA-AAAAAG
3585 AAAGAAAA
1 AAAGAAAA
3593 TATGGGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAAGAAAAAAG
Found at i:4265 original size:11 final size:11
Alignment explanation
Indices: 4235--4277 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4225 TTTTTGTTGA
*
4235 AAAAGGAAAA-
1 AAAAGAAAAAT
*
4245 AAATGAAAAAT
1 AAAAGAAAAAT
4256 AAATAGAAAAAT
1 AAA-AGAAAAAT
4268 AAAAGAAAAA
1 AAAAGAAAAA
4278 AGAAGAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (11 bp):
AAAAGAAAAAT
Found at i:4278 original size:12 final size:12
Alignment explanation
Indices: 4241--4277 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
4231 TTGAAAAAGG
4241 AAAA-AAAT-GA
1 AAAATAAATAGA
4251 AAAATAAATAGA
1 AAAATAAATAGA
4263 AAAATAAA-AGA
1 AAAATAAATAGA
4274 AAAA
1 AAAA
4278 AGAAGAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (12 bp):
AAAATAAATAGA
Found at i:7210 original size:16 final size:16
Alignment explanation
Indices: 7191--7229 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
7181 TAAATAGTAT
7191 AAAAAATATAAAAAAA
1 AAAAAATATAAAAAAA
*
7207 AAAAAATATATAAAAA
1 AAAAAATATAAAAAAA
*
7223 TAAAAAT
1 AAAAAAT
7230 GTATGTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAATATAAAAAAA
Found at i:7212 original size:18 final size:19
Alignment explanation
Indices: 7191--7228 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
7181 TAAATAGTAT
7191 AAAAAATATAAAAA-AAAA
1 AAAAAATATAAAAATAAAA
*
7209 AAAATATATAAAAATAAAA
1 AAAAAATATAAAAATAAAA
7228 A
1 A
7229 TGTATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAATATAAAAATAAAA
Found at i:7388 original size:12 final size:12
Alignment explanation
Indices: 7371--7395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7361 ATACGTTAGG
7371 AAAATATAGTAA
1 AAAATATAGTAA
7383 AAAATATAGTAA
1 AAAATATAGTAA
7395 A
1 A
7396 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATAGTAA
Found at i:7431 original size:2 final size:2
Alignment explanation
Indices: 7424--7577 Score: 111
Period size: 2 Copynumber: 78.5 Consensus size: 2
7414 AATAATAATA
7424 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
* * * ** * * * *
7466 AT AT AT AT AT AT A- AT AGG A- AA AT AT AT A- AC GC AA AG AA AA
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
7506 AT GAA AA AA AT AT A- AT AA AT AA AT AT AA AT AT A- 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
*
7547 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7578 AATAATAAGG
Statistics
Matches: 127, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
1 5 0.04
2 120 0.94
3 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (2 bp):
AT
Found at i:8071 original size:37 final size:37
Alignment explanation
Indices: 7978--8079 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
7968 ATGCTCGTGG
* * ** * * *
7978 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTAT
*
8015 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTAT
8052 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
8080 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTAT
Found at i:9014 original size:106 final size:106
Alignment explanation
Indices: 8830--9999 Score: 1822
Period size: 106 Copynumber: 11.0 Consensus size: 106
8820 GCATTGTTCC
* * * * * *
8830 GAGTCTAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
8894 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
8936 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
9001 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
9042 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
9107 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
9148 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCCGAAATTGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
9213 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
9254 GAGTCCAATATCTTTCGCTGTGAAATTGAAATTGGCTCCGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
9319 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
9360 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
9425 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
9466 GAGTCCAATATCCTTGGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
9531 CCAGCGCTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
9572 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCTGAAAATT-GGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AAATTGGGAAGTTGTTTGTTGACA
* *
9636 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
9678 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
9743 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
9784 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
9849 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
9890 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTCGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
9955 CTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
9996 GAGT
1 GAGT
10000 GGCACGATAT
Statistics
Matches: 984, Mismatches: 77, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
105 5 0.01
106 973 0.99
107 6 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:10540 original size:18 final size:19
Alignment explanation
Indices: 10511--10547 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
10501 TGTTGAATCC
10511 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
10530 CCAAA-AATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
10548 TTGATGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.19
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:11627 original size:13 final size:13
Alignment explanation
Indices: 11611--11656 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
11601 TTCTTTTTGA
11611 TTTTTGTTCTTTC
1 TTTTTGTTCTTTC
11624 TTTTTGTTC-TTC
1 TTTTTGTTCTTTC
11636 TTTTTTGTTTCTTTTC
1 -TTTTTG-TTC-TTTC
11652 TTTTT
1 TTTTT
11657 TATTTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 15 0.52
14 3 0.10
15 5 0.17
16 3 0.10
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTGTTCTTTC
Found at i:11652 original size:16 final size:15
Alignment explanation
Indices: 11598--11675 Score: 61
Period size: 16 Copynumber: 5.0 Consensus size: 15
11588 TTTTTGTCCC
11598 TTTTTC-TTTTTGATT
1 TTTTTCTTTTTTG-TT
11613 TTTGTTCTTTCTTT-TT
1 TTT-TTCTTT-TTTGTT
*
11629 GTTCTTCTTTTTTGTT
1 -TTTTTCTTTTTTGTT
*
11645 TCTTTTCTTTTTTATT
1 T-TTTTCTTTTTTGTT
* *
11661 TTTTCCCTTTTTGTT
1 TTTTTCTTTTTTGTT
11676 CTGATTGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 18 0.35
16 26 0.51
17 4 0.08
18 3 0.06
ACGTcount: A:0.03, C:0.13, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTGTT
Found at i:15165 original size:19 final size:19
Alignment explanation
Indices: 15132--15168 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15122 TGCAGATGAT
15132 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
15151 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
15169 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:16690 original size:12 final size:12
Alignment explanation
Indices: 16673--16697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16663 TAACGTTAGG
16673 AAAATATAGTAA
1 AAAATATAGTAA
16685 AAAATATAGTAA
1 AAAATATAGTAA
16697 A
1 A
16698 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATAGTAA
Found at i:18143 original size:44 final size:44
Alignment explanation
Indices: 18056--18542 Score: 674
Period size: 44 Copynumber: 11.1 Consensus size: 44
18046 TTATTCATTA
* * *
18056 ATTTCATTTATGGCATCCTTTTATGCCTTTAATGTACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCC-TTAATGCACCATTATGC
* * ** *
18101 ATTTCATTTATGACATCTTTTCACACCTTAATGCATCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* * *
18145 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCACCGTTATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
*
18189 ATGTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
*
18233 A-TTCATTTAT-GCATCCTTTTATGCCTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* * *
18275 ATTTCATTTATGGCATCCTTTTATGCCTTAATGCACCGTTATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* * * *
18319 ATTTCATTTATGGCATCCTTTCATACCTTATTGAACCATTATGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* *
18363 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* *
18407 ATTTCATTTATGGCATCCTTTCTTTCCTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* *
18451 ATTTCATTTATGGCATCCTTTCATGACTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
* **
18495 ATTTCATTTATTGCATCAATTCAAT-CCTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTC-ATGCCTTAATGCACCATTATGC
18539 ATTT
1 ATTT
18543 TAACTATTAA
Statistics
Matches: 391, Mismatches: 48, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
42 32 0.08
43 17 0.04
44 318 0.81
45 24 0.06
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (44 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCACCATTATGC
Found at i:20129 original size:44 final size:44
Alignment explanation
Indices: 20081--20282 Score: 296
Period size: 44 Copynumber: 4.6 Consensus size: 44
20071 AACACACATT
* * * * *
20081 ATGCCTTAATGCACTGTTATGTATTTCATTTACGTCATCCTTTT
1 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
20125 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
1 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
* * *
20169 ATGCCTTAATGTACCATTATGCATTTAATTTATGGCATCCTTTC
1 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
20213 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
1 ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
* * **
20257 ATTCCTTAACGCACTATTATGCATTT
1 ATGCCTTAATGCACCGTTATGCATTT
20283 TAACTATTAA
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 143 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (44 bp):
ATGCCTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTC
Found at i:20290 original size:16 final size:17
Alignment explanation
Indices: 20269--20301 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20259 TCCTTAACGC
20269 ACTATT-ATGCATTTTA
1 ACTATTAATGCATTTTA
*
20285 ACTATTAATTCATTTTA
1 ACTATTAATGCATTTTA
20302 GAGCAGTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
ACTATTAATGCATTTTA
Found at i:26036 original size:737 final size:736
Alignment explanation
Indices: 24624--26094 Score: 2879
Period size: 737 Copynumber: 2.0 Consensus size: 736
24614 CAAGAATCAT
24624 ATCACTCTTTCTAACATGTTTTTAATCATGTCTAATGTTTCTAATCTCTAATTCACACCTCTGAC
1 ATCACTCTTTCTAACATGTTTTTAATCATGTCTAATGTTTCTAATCTCTAATTCACACCTCTGAC
24689 AAGTTAATTATACTAATAAACCTCAATAAAAACTCATATATCAACATATCATTGAAAAACTCATT
66 AAGTTAATTATACTAATAAACCTCAATAAAAACTCATATATCAACATATCATTGAAAAACTCATT
24754 TTCTTAAATCTCATATAAAACATCCACCTCTTAGTTTTAATCTTCTCTAACCCTTCCTTAAGTTT
131 TTCTTAAATCTCATATAAAACATCCACCTCTTAGTTTTAATCTTCTCTAACCCTTCCTTAAGTTT
*
24819 ACACATCGCTTAAAGTTACAAGATTAACCCATAATAGGAAGGAAGAACTAGTTAAATGAATTTAC
196 ACACATCGCTTAAAGTTACAAGAGTAACCCATAATAGGAAGGAAGAACTAGTTAAATGAATTTAC
24884 CTTATTACTAGAAATTCATTTTTAAGGGTTTGGGAGTCGATTATAAGTGGGGAAAGATTAACACC
261 CTTATTACTAGAAATTCATTTTTAAGGGTTTGGGAGTCGATTATAAGTGGGGAAAGATTAACACC
24949 CCCACAACGCCCAAAATTGGTACATCTCGATTTTGATGACTTTTGAATAATGAGTGAATCTATTT
326 CCCACAACGCCCAAAATTGGTACATCTCGATTTTGATGACTTTTGAATAATGAGTGAATCTATTT
*
25014 TATGATATTTGTCTCAATGAACATGATTTAATTAACTCGATTTTATTTAATAATGATGTCTCCTT
391 TATGATATTTGTCTCAATGAACATGATTTAATTAACTCGATTTTATTTAAGAATGATGTCTCCTT
*
25079 ACTACATGAATTAATAGAAATTGAAATCCAGTCATGTTGGATGTAATTTCGTTAACCCACAATGC
456 ACTACATGAATTAATAGAAATTGAAATCCAGTCATGTTGGACGTAATTTCGTTAACCCACAATGC
25144 AAGACAACATTGCCATTGATTAATTTGGAAAATGAGAAAATAAATGCATGATGCATGAGTGCATC
521 AAGACAACATTGCCATTGATTAATTTGGAAAATGAGAAAATAAATGCATGATGCATGAGTGCATC
* *
25209 AATAATAGATGCCATGCACAAGATAGATTAAATATTGAACGTAATGTAACAGATGGATAATAAAA
586 AATAATAGATGCCATGCACAAGATAGATGAAATATTGAACATAATGTAACAGATGGATAATAAAA
25274 ATAACGAAATAATAAATAAAACCAACAATGAATATCTATTTTATTAAAATGATTTCACTTCGTAA
651 ATAACGAAATAATAAATAAAACCAACAATGAATATCTATTTTATTAAAATGATTTCACTTCGTAA
25339 AAAATAAAAATGTCAAAAGTC
716 AAAATAAAAATGTCAAAAGTC
25360 ATCACTCTTTCTAACATGTTTTTAATCATGTCTAATGTTTCTAATCTCTAATTCACACCTCTGAC
1 ATCACTCTTTCTAACATGTTTTTAATCATGTCTAATGTTTCTAATCTCTAATTCACACCTCTGAC
25425 AAGTTAATTATACTAATAAACCTCAATAAAAACTCATATATCAACATATCATTGAAAAACTCATT
66 AAGTTAATTATACTAATAAACCTCAATAAAAACTCATATATCAACATATCATTGAAAAACTCATT
25490 TTCTTAAATCTCATATAAAACATCCACCTCTTAGTTTTAATCTTCTCTAACCCTTCCTTAAGTTT
131 TTCTTAAATCTCATATAAAACATCCACCTCTTAGTTTTAATCTTCTCTAACCCTTCCTTAAGTTT
25555 ACACATCGCTTAAAGTTACAAGAGTAACCCATAATAGGAAGGAAGAACTAGTTAAATGAAGTTTA
196 ACACATCGCTTAAAGTTACAAGAGTAACCCATAATAGGAAGGAAGAACTAGTTAAATGAA-TTTA
25620 CCTTATTACTAGAAATTCATTTTTAAGGGTTTGGGAGTCGATTATAAGTGGGGAAAGATTAACAC
260 CCTTATTACTAGAAATTCATTTTTAAGGGTTTGGGAGTCGATTATAAGTGGGGAAAGATTAACAC
25685 CCCCACAACGCCCAAAATTGGTACATCTCGATTTTGATGACTTTTGAATAATGAGTGAATCTATT
325 CCCCACAACGCCCAAAATTGGTACATCTCGATTTTGATGACTTTTGAATAATGAGTGAATCTATT
*
25750 TTATGATATTTGTCTCAATGAACATGATTTAATTAATTCGATTTTATTTAAGAATGATGTCTCCT
390 TTATGATATTTGTCTCAATGAACATGATTTAATTAACTCGATTTTATTTAAGAATGATGTCTCCT
25815 TACTACATGAATTAATAGAAATTGAAATCCAGTCATGTTGGACGTAATTTCGTTAACCCACAATG
455 TACTACATGAATTAATAGAAATTGAAATCCAGTCATGTTGGACGTAATTTCGTTAACCCACAATG
25880 CAAGACAACATTGCCATTGATTAATTTGGAAAATGAGAAAATAAATGCATGATGCATGAGTGCAT
520 CAAGACAACATTGCCATTGATTAATTTGGAAAATGAGAAAATAAATGCATGATGCATGAGTGCAT
25945 CAATAATAGATGCCATGCACAAGATAGATGAAATATTGAACATAATGTAACAGATGGATAATAAA
585 CAATAATAGATGCCATGCACAAGATAGATGAAATATTGAACATAATGTAACAGATGGATAATAAA
26010 AATAACGAAATAATAAATAAAACCAACAATGAATATCTATTTTATTAAAATGATTTCACTTCGTA
650 AATAACGAAATAATAAATAAAACCAACAATGAATATCTATTTTATTAAAATGATTTCACTTCGTA
26075 AAAAATAAAAATGTCAAAAG
715 AAAAATAAAAATGTCAAAAG
26095 CTATACATTT
Statistics
Matches: 728, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
736 254 0.35
737 474 0.65
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (736 bp):
ATCACTCTTTCTAACATGTTTTTAATCATGTCTAATGTTTCTAATCTCTAATTCACACCTCTGAC
AAGTTAATTATACTAATAAACCTCAATAAAAACTCATATATCAACATATCATTGAAAAACTCATT
TTCTTAAATCTCATATAAAACATCCACCTCTTAGTTTTAATCTTCTCTAACCCTTCCTTAAGTTT
ACACATCGCTTAAAGTTACAAGAGTAACCCATAATAGGAAGGAAGAACTAGTTAAATGAATTTAC
CTTATTACTAGAAATTCATTTTTAAGGGTTTGGGAGTCGATTATAAGTGGGGAAAGATTAACACC
CCCACAACGCCCAAAATTGGTACATCTCGATTTTGATGACTTTTGAATAATGAGTGAATCTATTT
TATGATATTTGTCTCAATGAACATGATTTAATTAACTCGATTTTATTTAAGAATGATGTCTCCTT
ACTACATGAATTAATAGAAATTGAAATCCAGTCATGTTGGACGTAATTTCGTTAACCCACAATGC
AAGACAACATTGCCATTGATTAATTTGGAAAATGAGAAAATAAATGCATGATGCATGAGTGCATC
AATAATAGATGCCATGCACAAGATAGATGAAATATTGAACATAATGTAACAGATGGATAATAAAA
ATAACGAAATAATAAATAAAACCAACAATGAATATCTATTTTATTAAAATGATTTCACTTCGTAA
AAAATAAAAATGTCAAAAGTC
Found at i:26433 original size:2 final size:2
Alignment explanation
Indices: 26421--26465 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
26411 ATGGATGATA
26421 AT AT GAT 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
26464 AT
1 AT
26466 GAAAAAATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30635 original size:21 final size:22
Alignment explanation
Indices: 30598--30638 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
30588 TTAAATATTA
30598 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTATCGATACTCAT
*
30620 TAAAGG-AGTGTCGATACTC
1 TAAAGGAAGTATCGATACTC
30639 CCTATCCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTATCGATACTCAT
Found at i:32294 original size:3 final size:3
Alignment explanation
Indices: 32286--32320 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
32276 TATTAAAATA
* *
32286 AAT AAT AAT AAT AAT AAT AAC AAT GAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
32321 AGAATAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:45242 original size:6 final size:6
Alignment explanation
Indices: 45215--45251 Score: 53
Period size: 5 Copynumber: 6.7 Consensus size: 6
45205 GTTAAATAAT
45215 AAAATG -AAATG -AAATG -AAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
45252 ATAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 15 0.50
6 15 0.50
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:45961 original size:21 final size:20
Alignment explanation
Indices: 45932--45970 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
45922 TCTTTTGCTA
45932 TGTGTTTCT-TGTGTGGTTGC
1 TGTGTTTCTCT-TGTGGTTGC
45952 TGTGATTTCTCTTGTGGTT
1 TGTG-TTTCTCTTGTGGTT
45971 TTGTCTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.03, C:0.10, G:0.31, T:0.56
Consensus pattern (20 bp):
TGTGTTTCTCTTGTGGTTGC
Found at i:48132 original size:37 final size:37
Alignment explanation
Indices: 48090--48162 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
48080 TTATCGTTAA
**
48090 GTTGTTACTATAAATTAAAAGTAATACAATATTTATG
1 GTTGTTACTATAAAAAAAAAGTAATACAATATTTATG
*
48127 GTTGTTATTATAAAAAAAAAGTAATACAATATTTAT
1 GTTGTTACTATAAAAAAAAAGTAATACAATATTTAT
48163 AGGAGAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.40
Consensus pattern (37 bp):
GTTGTTACTATAAAAAAAAAGTAATACAATATTTATG
Found at i:51117 original size:21 final size:21
Alignment explanation
Indices: 51086--51143 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
51076 AATCCCTTTA
***
51086 AAAAGGATCGATCCCTCGTGGG
1 AAAA-GATCGATCCCTCGAAAG
*
51108 AAAAGATCGATCACTCGAAAG
1 AAAAGATCGATCCCTCGAAAG
51129 AAAAGATCGATCCCT
1 AAAAGATCGATCCCT
51144 TCTCTGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (21 bp):
AAAAGATCGATCCCTCGAAAG
Found at i:53200 original size:15 final size:14
Alignment explanation
Indices: 53180--53230 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
53170 ATCTCGTTTC
53180 TTTATTATTATATTT
1 TTTATTATT-TATTT
53195 TTTA-T-TTTATTT
1 TTTATTATTTATTT
*
53207 TTTATGAATTTATTT
1 TTTAT-TATTTATTT
*
53222 TCTATTATT
1 TTTATTATT
53231 GTTTATCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 4 0.13
15 15 0.50
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTATTATTTATTT
Found at i:59945 original size:20 final size:19
Alignment explanation
Indices: 59922--59965 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
59912 TTTAAATTAC
59922 TTTAGTCTTTAAAATTTTAT
1 TTTA-TCTTTAAAATTTTAT
*
59942 TTTATGTTTAAAATTTTAT
1 TTTATCTTTAAAATTTTAT
59961 TTTAT
1 TTTAT
59966 GTTAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTATCTTTAAAATTTTAT
Found at i:59972 original size:18 final size:19
Alignment explanation
Indices: 59929--59973 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
59919 TACTTTAGTC
59929 TTTAAAATTTTATTTTATG
1 TTTAAAATTTTATTTTATG
59948 TTTAAAATTTTATTTTATG
1 TTTAAAATTTTATTTTATG
59967 -TTAAAAT
1 TTTAAAAT
59974 CATTTATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTAAAATTTTATTTTATG
Found at i:66577 original size:37 final size:37
Alignment explanation
Indices: 66501--66577 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
66491 TTTTTATATT
*
66501 TTTAATTTTGTAAAACAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAACAAATTATATAAATATTATCAA
* *
66538 TTTAATTTTTTAAATA-AAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-ACAAATTATATAAATATTAT-CAA
66575 TTT
1 TTT
66578 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAACAAATTATATAAATATTATCAA
Found at i:68451 original size:2 final size:2
Alignment explanation
Indices: 68446--68483 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
68436 CCACACACAC
68446 AT AT AT AT AT GAT 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 AT AT AT AT A
68484 GGCTCAACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76410 original size:2 final size:2
Alignment explanation
Indices: 76403--76449 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
76393 CCATTCAACT
76403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76445 TA TA T
1 TA TA T
76450 CTTTCTATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76914 original size:27 final size:27
Alignment explanation
Indices: 76864--76915 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
76854 CATACAAACC
* *
76864 CTCTCAAAACTCAAACTCTCTTAAATT
1 CTCTCAAAACTCAAACTATATTAAATT
* *
76891 CTCTCAAAGCTCAAATTATATTAAA
1 CTCTCAAAACTCAAACTATATTAAA
76916 AAAGTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (27 bp):
CTCTCAAAACTCAAACTATATTAAATT
Found at i:77107 original size:16 final size:16
Alignment explanation
Indices: 77068--77111 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
77058 ATTTGCTAAC
77068 TATTTTAAT-TTTAAT
1 TATTTTAATATTTAAT
77083 TATTGTTAATATTTAAT
1 TATT-TTAATATTTAAT
77100 T-TGTTTAATATT
1 TAT-TTTAATATT
77112 AGTTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 14 0.54
17 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TATTTTAATATTTAAT
Found at i:77135 original size:27 final size:25
Alignment explanation
Indices: 77068--77138 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
77058 ATTTGCTAAC
*
77068 TATTTTAATTTTA-ATTATTGTTAA
1 TATTTTAATTTTATAATATTGTTAA
* *
77092 TA-TTTAATTTGTTTAATATTAGTTTA
1 TATTTTAATTT-TATAATATT-GTTAA
77118 TATTTTAATTTCTATAATATT
1 TATTTTAATTT-TATAATATT
77139 TATTAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 8 0.21
24 3 0.08
25 5 0.13
26 6 0.16
27 16 0.42
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (25 bp):
TATTTTAATTTTATAATATTGTTAA
Found at i:79863 original size:21 final size:21
Alignment explanation
Indices: 79821--79873 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
79811 ATTCTGACTA
79821 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* ** *
79842 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
79863 TCGCAATGCGA
1 TCGCATTGCGA
79874 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:79888 original size:20 final size:20
Alignment explanation
Indices: 79863--79956 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
79853 TTTTTCTAAT
79863 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
79883 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
79903 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
79924 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
79944 TCGCAATGCGAAT
1 TCGCAATGCGAAT
79957 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:79894 original size:41 final size:41
Alignment explanation
Indices: 79863--79956 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
79853 TTTTTCTAAT
*
79863 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGATTACGTAAA
* * *
79903 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGATTACGTAAA
79944 TCGCAATGCGAAT
1 TCGCAATGCGAAT
79957 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 12 0.24
41 37 0.76
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGATTACGTAAA
Found at i:80524 original size:20 final size:20
Alignment explanation
Indices: 80499--80620 Score: 118
Period size: 19 Copynumber: 6.5 Consensus size: 20
80489 TTCTAAACTT
80499 AAAATCGCAACATGA-AAATG
1 AAAATCGCAACA-GAGAAATG
* *
80519 AAAATCGCAACACAAAAATG
1 AAAATCGCAACAGAGAAATG
**
80539 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGAGAAATG
80560 AAAATCGCAAC-GAGAAATG
1 AAAATCGCAACAGAGAAATG
80579 AAAATCGCAAC-GAG--AT-
1 AAAATCGCAACAGAGAAATG
*
80595 --AATCGCAAC-GTGAAATG
1 AAAATCGCAACAGAGAAATG
80612 AAAATCGCA
1 AAAATCGCA
80621 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.13
16 2 0.02
17 2 0.02
19 30 0.34
20 26 0.30
21 16 0.18
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACAGAGAAATG
Found at i:80560 original size:21 final size:21
Alignment explanation
Indices: 80499--80593 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 21
80489 TTCTAAACTT
80499 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
* *
80519 AAAATCGCAAC-ACAAAAATG
1 AAAATCGCAACGAGAGAAATG
**
80539 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
80560 AAAATCGCAAC--GAGAAATG
1 AAAATCGCAACGAGAGAAATG
80579 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
80594 TAATCGCAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 20 0.31
20 26 0.41
21 18 0.28
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:80578 original size:40 final size:40
Alignment explanation
Indices: 80499--80593 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
80489 TTCTAAACTT
80499 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACAAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACAAAAATG
** * *
80539 ACTATCGCAACGAGAGAAATGAAAATCGCAAC-GAGAAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACAAAAATG
80579 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
80594 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 30 0.64
41 17 0.36
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACAAAAATG
Found at i:80645 original size:19 final size:19
Alignment explanation
Indices: 80616--80714 Score: 110
Period size: 20 Copynumber: 5.1 Consensus size: 19
80606 GAAATGAAAA
* *
80616 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
80635 TCTCGTTGCGATTTTTC-TT
1 TCGCGTTGCGA-TTTTCATT
**
80654 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
80673 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
80693 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
80713 TC
1 TC
80715 AACCAAAAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
18 3 0.04
19 26 0.39
20 37 0.55
21 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:82993 original size:94 final size:94
Alignment explanation
Indices: 82407--82970 Score: 883
Period size: 94 Copynumber: 6.1 Consensus size: 94
82397 TATATTGCTT
* * * *
82407 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
82468 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* * *
82497 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
82562 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
82591 AGTAAATTTGA-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTT-ATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAG
*
82655 TATTTGTATTTGTTTTGTCTTTAT-GTTGAA
65 TATTTGTCTTTGTTTTGTCTTT-TGGTTGAA
* * * *
82685 AGTAAATTTGTTCGTTTGCTGCCAATTCTACTAAATTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
82750 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
82779 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
82844 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
82873 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
82938 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
82966 AGTAA
1 AGTAA
82971 TGCAATCCAT
Statistics
Matches: 451, Mismatches: 14, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
90 35 0.08
92 3 0.01
93 29 0.06
94 382 0.85
95 2 0.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:83103 original size:39 final size:38
Alignment explanation
Indices: 83060--83157 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 38
83050 GTCTTTTGGT
83060 TGAAATGAAAATCGCAACG-AGAGAATGAAAATCGCAACG
1 TGAAATGAAAATCGCAACGCA-A-AATGAAAATCGCAACG
83099 TGAAATGAAAATCGCAACGCAAAATGAAAATCGCAACG
1 TGAAATGAAAATCGCAACGCAAAATGAAAATCGCAACG
* **
83137 CGAAACCAAAAATCGCAACGC
1 TGAAA-TGAAAATCGCAACGC
83158 GAAACTATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
38 20 0.37
39 33 0.61
40 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (38 bp):
TGAAATGAAAATCGCAACGCAAAATGAAAATCGCAACG
Found at i:83107 original size:19 final size:19
Alignment explanation
Indices: 83061--83161 Score: 139
Period size: 19 Copynumber: 5.2 Consensus size: 19
83051 TCTTTTGGTT
*
83061 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
83080 GAGAATGAAAATCGCAACGT
1 GA-AATGAAAATCGCAACGC
83100 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
83119 AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
83138 GAAACCAAAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGC
83158 GAAA
1 GAAA
83162 CTATAATCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.53
20 35 0.47
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:83171 original size:19 final size:20
Alignment explanation
Indices: 83061--83163 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
83051 TCTTTTGGTT
*
83061 GAAA-TGAAAATCGCAACGA
1 GAAACTGAAAATCGCAACGC
*
83080 GAGAA-TGAAAATCGCAACGT
1 GA-AACTGAAAATCGCAACGC
83100 GAAA-TGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
*
83119 -AAAATGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
**
83138 GAAACCAAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
83158 GAAACT
1 GAAACT
83164 ATAATCGCGT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
18 3 0.04
19 33 0.44
20 39 0.52
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACGC
Found at i:83190 original size:19 final size:19
Alignment explanation
Indices: 83168--83312 Score: 122
Period size: 19 Copynumber: 7.8 Consensus size: 19
83158 GAAACTATAA
*
83168 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
* *
83187 TCGCATTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
83203 T--CGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
*
83219 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
* *
83238 TTGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
83257 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
* **
83277 TCGTGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
83298 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
83313 AAGTTCCAGA
Statistics
Matches: 97, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 2 0.02
18 12 0.12
19 41 0.42
20 16 0.16
21 13 0.13
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:83286 original size:39 final size:38
Alignment explanation
Indices: 83168--83312 Score: 113
Period size: 39 Copynumber: 3.9 Consensus size: 38
83158 GAAACTATAA
* * * *
83168 TCGCGTTGCGATTTTAATTTCGCATTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
* *
83203 T--CGTTGCGATTTT-ATTTCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
* * *
83238 TTGCATTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCACGTTGCGATTTTCATT
* **
83277 TCGTGTTGCGATAGTCATTTTTCACGTTGCGATTTT
1 TCGCGTTGCGATTTTCA--TTTCACGTTGCGATTTT
83313 AAGTTCCAGA
Statistics
Matches: 90, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
32 13 0.14
33 12 0.13
34 3 0.03
35 3 0.03
37 11 0.12
38 3 0.03
39 29 0.32
40 14 0.16
41 2 0.02
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
Found at i:83789 original size:21 final size:21
Alignment explanation
Indices: 83765--83831 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
83755 TCATTCCTCG
83765 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
83786 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
83807 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
83828 AGAG
1 AGAG
83832 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:83789 original size:42 final size:42
Alignment explanation
Indices: 83713--83831 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
83703 GAATCGCCTG
* * * * * * *
83713 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
83755 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
83797 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
83832 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:85200 original size:14 final size:14
Alignment explanation
Indices: 85181--85216 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
85171 ATTGTTTAAT
85181 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
85195 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
85209 TGATTTGT
1 TGATTTGT
85217 TTAATTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:85339 original size:19 final size:17
Alignment explanation
Indices: 85323--85370 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 17
85313 AAAAATGACT
85323 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
85342 ATCGCAA--CGAAA-GA
1 ATCGCAATGCGAAATGA
85356 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
85371 AAAAATCGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.31
16 6 0.23
17 5 0.19
19 7 0.27
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.15
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:85365 original size:33 final size:32
Alignment explanation
Indices: 85323--85416 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 32
85313 AAAAATGACT
85323 ATCGCAATGCGAAATGAAAATCGCAACGA-AAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAA-A
85356 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
* *
85389 ATCGCAACGTGAAACTAAAATCGCAACG
1 ATCGCAATGCGAAA-TAAAATCGCAACG
85417 CGAAACTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 53 0.95
34 3 0.05
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:85379 original size:19 final size:19
Alignment explanation
Indices: 85323--85381 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
85313 AAAAATGACT
*
85323 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
*
85342 ATCGCAA--CG--A-AAGA
1 ATCGCAATGCGAAATAAAA
85356 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
85375 ATCGCAA
1 ATCGCAA
85382 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:85410 original size:19 final size:19
Alignment explanation
Indices: 85355--85423 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
85345 GCAACGAAAG
*
85355 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
85374 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
85388 AATCGCAACGTGAAACTAA
1 AATCGCAACGCGAAACTAA
85407 AATCGCAACGCGAAACT
1 AATCGCAACGCGAAACT
85424 TAATTCATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 1 0.02
17 2 0.05
18 2 0.05
19 26 0.62
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:85479 original size:33 final size:33
Alignment explanation
Indices: 85432--85595 Score: 220
Period size: 33 Copynumber: 4.8 Consensus size: 33
85422 CTTAATTCAT
* * *
85432 GTTGCGATTTTCATTTCGCTTTACGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
85465 GTTGTGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
85498 GTTGCGATTTTCATTTCGCATTGCGATTCTCTT
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* *
85531 GTTGCGATTTTCATTTCACATTGCGATTTTCATTTC
1 GTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTC
85567 GCATTGCGATTTTCATTTCGCATTGCGAT
1 G--TTGCGATTTTCATTTCGCATTGCGAT
85596 AGTCATTTCT
Statistics
Matches: 116, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
33 85 0.73
35 3 0.03
36 4 0.03
38 24 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:85523 original size:19 final size:19
Alignment explanation
Indices: 85470--85615 Score: 159
Period size: 19 Copynumber: 8.2 Consensus size: 19
85460 CCCTCGTTGT
85470 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
85489 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
85503 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
85522 GATTCTC--TT-G--TTGC
1 GATTTTCATTTCGCATTGC
*
85536 GATTTTCATTTCACATTGC
1 GATTTTCATTTCGCATTGC
85555 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
85574 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
** *
85593 GATAGTCATTTCTGCGTTGC
1 GATTTTCATTTC-GCATTGC
85613 GAT
1 GAT
85616 AGACATTAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
14 16 0.15
16 10 0.09
17 9 0.08
19 63 0.59
20 9 0.08
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:86295 original size:2 final size:2
Alignment explanation
Indices: 86288--86325 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
86278 AATGTTAGAA
86288 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
86326 TTTAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88263 original size:84 final size:83
Alignment explanation
Indices: 88167--88429 Score: 259
Period size: 84 Copynumber: 3.2 Consensus size: 83
88157 GAGTGTAATT
* *
88167 GAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTTTCGACTTCAGCTATGCTTCAAATGATGTGC
1 GAACTCGAAGGTCTT-GGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGC
88232 CTTGGAGCTGAGCGTAGTC
65 CTTGGAGCTGAGCGTAGTC
** * * * * * * *
88251 GAACTCGAAGGTCTTTGG-TCACAGATAACCCTTGTAGCCTTGAGTTATGCTGT-AAATGATATA
1 GAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT-TCAAATGATGT-
* * * * *
88314 CCCTCGAAGCTGAGTGTAATC
63 GCCTTGGAGCTGAGCGTAGTC
** *
88335 GAACTCGGGGGTC-T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 GAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCC
88397 ATT-GAGCTGAGCGTAGTC
66 -TTGGAGCTGAGCGTAGTC
*
88415 GAACTCAAAGGTCTT
1 GAACTCGAAGGTCTT
88430 TTGTTAGCAG
Statistics
Matches: 138, Mismatches: 34, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
80 24 0.17
81 35 0.25
82 1 0.01
83 33 0.24
84 43 0.31
85 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (83 bp):
GAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCC
TTGGAGCTGAGCGTAGTC
Found at i:88819 original size:106 final size:106
Alignment explanation
Indices: 88630--89653 Score: 1661
Period size: 106 Copynumber: 9.6 Consensus size: 106
88620 TATTGTTCTA
* * * *
88630 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
88695 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
88736 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
88801 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
88842 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
88907 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
88948 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* *
89013 TAGCGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
89054 AGTCCAATATCCTCCGCTGGGAAGTTTGAAATTGGCTCTGAAATTGGGAGGTTGTTTTTTTTTTT
1 AGTCCAATATCCTTCGCTGTGAAG-TTGAAATTGGCTCTGAAATTGGGAAATTG------TTTGT
*
89119 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
59 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
89167 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
89232 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
89273 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
89338 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
89379 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTCTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
89444 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
89485 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTCTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
89550 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
89591 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTCTGTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
89654 GACAACTTTT
Statistics
Matches: 867, Mismatches: 44, Indels: 14
0.94 0.05 0.02
Matches are distributed among these distances:
106 743 0.86
107 27 0.03
112 26 0.03
113 71 0.08
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:93169 original size:11 final size:11
Alignment explanation
Indices: 93149--93179 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
93139 AATTGCGAAA
93149 AAAATTAAATT
1 AAAATTAAATT
*
93160 AAATTTAAATT
1 AAAATTAAATT
93171 AAAATTAAA
1 AAAATTAAA
93180 AAAAACTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:97077 original size:24 final size:24
Alignment explanation
Indices: 97026--97077 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
97016 ATCTGAGTAT
** *
97026 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
97050 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
97074 TGAC
1 TGAC
97078 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:97949 original size:20 final size:21
Alignment explanation
Indices: 97925--98065 Score: 157
Period size: 20 Copynumber: 7.0 Consensus size: 21
97915 CAGAATCTCG
97925 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
97945 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* * * *
97965 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
97986 TTGCGATTTACGT-AATCACA
1 TTGCGATTTACGTAAATCGCA
98006 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
*
98026 TTGCGATTTACGT-ATTCGCA
1 TTGCGATTTACGTAAATCGCA
* * *
98046 TTGCGAATTAGGAAAATCGC
1 TTGCGATTTACGTAAATCGC
98066 GACGCGAATT
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.04
20 74 0.71
21 26 0.25
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:97981 original size:21 final size:20
Alignment explanation
Indices: 97926--98093 Score: 113
Period size: 20 Copynumber: 8.2 Consensus size: 20
97916 AGAATCTCGT
* *
97926 TGCGATTTACTAAATCGCAA
1 TGCGAATTACGAAATCGCAA
97946 TGCG-ATTACGTAAATCGCAA
1 TGCGAATTACG-AAATCGCAA
* *
97966 TGCGAATTAGGAAAATCGCAT
1 TGCGAATTACG-AAATCGCAA
* * * *
97987 TGCGATTTACGTAATCACAT
1 TGCGAATTACGAAATCGCAA
* * *
98007 TGCGATTTACGTAATCGCAT
1 TGCGAATTACGAAATCGCAA
* * * *
98027 TGCGATTTACGTATTCGCAT
1 TGCGAATTACGAAATCGCAA
* *
98047 TGCGAATTAGGAAAATCGCGA
1 TGCGAATTACG-AAATCGCAA
* **
98068 CGCGAATTTGGGAAATCGCAA
1 TGCGAA-TTACGAAATCGCAA
98089 TGCGA
1 TGCGA
98094 TAGTCAGAAT
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
19 4 0.03
20 71 0.58
21 44 0.36
22 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCGAATTACGAAATCGCAA
Found at i:101013 original size:32 final size:33
Alignment explanation
Indices: 100969--101046 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
100959 GATGATACAG
* * *
100969 GCAAACACGAAGAGGAGGAACAGGATGAAGG-A
1 GCAAACATGAAGAGGAGCAACAGGAAGAAGGTA
* *
101001 GTAAACATGAAGAGGAGCAGCAGGAAGAAGGTA
1 GCAAACATGAAGAGGAGCAACAGGAAGAAGGTA
101034 GCAAACATGAAGA
1 GCAAACATGAAGA
101047 AGAAGAGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 26 0.67
33 13 0.33
ACGTcount: A:0.47, C:0.12, G:0.35, T:0.06
Consensus pattern (33 bp):
GCAAACATGAAGAGGAGCAACAGGAAGAAGGTA
Found at i:101045 original size:18 final size:17
Alignment explanation
Indices: 100969--101048 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 17
100959 GATGATACAG
*
100969 GCAAACACGAAG-AGGA
1 GCAAACATGAAGAAGGA
* * *
100985 G-GAACAGGATGAAGGA
1 GCAAACATGAAGAAGGA
*
101001 GTAAACATGAAG-AGGA
1 GCAAACATGAAGAAGGA
* *
101017 GC-AGCAGGAAGAAGGTA
1 GCAAACATGAAGAAGG-A
101034 GCAAACATGAAGAAG
1 GCAAACATGAAGAAG
101049 AAGAGGAGCC
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
15 14 0.29
16 14 0.29
17 10 0.21
18 10 0.21
ACGTcount: A:0.47, C:0.11, G:0.35, T:0.06
Consensus pattern (17 bp):
GCAAACATGAAGAAGGA
Found at i:106361 original size:17 final size:16
Alignment explanation
Indices: 106339--106370 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
106329 ATTAAGTTAC
106339 AGAGTGAAGAAGGGAAA
1 AGAGTGAAG-AGGGAAA
106356 AGAGTGAAGAGGGAA
1 AGAGTGAAGAGGGAA
106371 TGAGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (16 bp):
AGAGTGAAGAGGGAAA
Found at i:110868 original size:15 final size:15
Alignment explanation
Indices: 110850--110879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
110840 AAAACCATGT
*
110850 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
110865 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
110880 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:111004 original size:21 final size:21
Alignment explanation
Indices: 110978--111038 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
110968 AAATAAATAT
*
110978 AAAAAATAAAGAAA-AAGAAGA
1 AAAAAATAAAGAAATAA-AACA
*
110999 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAATAAAACA
*
111020 AATAAATAAA-ATAATAAAA
1 AAAAAATAAAGA-AATAAAA
111039 AAAGTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.91
22 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAAAATAAAGAAATAAAACA
Found at i:111065 original size:49 final size:47
Alignment explanation
Indices: 110966--111083 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 47
110956 AAATAGTAAG
110966 TAAAATAAATATAA-AAAATAAAGAAAAAGAAGAAAAAAATATAGAAA
1 TAAAATAAATA-AATAAAATAAAGAAAAAGAAGAAAAAAATATAGAAA
* * *
111013 TAAAACAAATAAATAAAAT-AATAAAAA-AAGTAAAAATAATATATATATA
1 TAAAATAAATAAATAAAATAAAGAAAAAGAAG-AAAAA-AATATAGA-A-A
*
111062 TAAAATAAAAAAATAAAA-AAAG
1 TAAAATAAATAAATAAAATAAAG
111084 TAAATATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
45 3 0.05
46 14 0.24
47 22 0.37
48 1 0.02
49 19 0.32
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (47 bp):
TAAAATAAATAAATAAAATAAAGAAAAAGAAGAAAAAAATATAGAAA
Found at i:111079 original size:32 final size:33
Alignment explanation
Indices: 111032--111095 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
111022 TAAATAAAAT
*
111032 AATAAAAAAAGTAAAAATAA-TATATATATATAA
1 AATAAAAAAAGTAAAAA-AAGTAAATATATATAA
111065 AATAAAAAAA-TAAAAAAAGTAAATATATATA
1 AATAAAAAAAGTAAAAAAAGTAAATATATATA
111096 TATATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 17 0.59
33 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (33 bp):
AATAAAAAAAGTAAAAAAAGTAAATATATATAA
Found at i:111087 original size:9 final size:8
Alignment explanation
Indices: 110967--111087 Score: 57
Period size: 9 Copynumber: 14.0 Consensus size: 8
110957 AATAGTAAGT
110967 AAAATAAA
1 AAAATAAA
110975 TATAAA-AAA
1 -A-AAATAAA
* *
110984 TAAAGAAA
1 AAAATAAA
*
110992 AAGAAGAAA
1 AA-AATAAA
*
111001 AAAATATA
1 AAAATAAA
*
111009 GAAATAAA
1 AAAATAAA
111017 ACAAATAAA
1 A-AAATAAA
111026 TAAAATAATA
1 -AAAATAA-A
111036 AAAA-AAGTA
1 AAAATAA--A
111045 AAAATAATA
1 AAAATAA-A
* * *
111054 TATATATAT
1 AAAATA-AA
111063 AAAATAAA
1 AAAATAAA
111071 AAAATAAA
1 AAAATAAA
111079 AAAAGTAAA
1 AAAA-TAAA
111088 TATATATATA
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
7 3 0.03
8 29 0.33
9 49 0.55
10 8 0.09
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:111090 original size:36 final size:37
Alignment explanation
Indices: 111000--111164 Score: 130
Period size: 36 Copynumber: 4.4 Consensus size: 37
110990 AAAAGAAGAA
* * * *
111000 AAAAAT-ATAGAAATAAA-ACAAATAAATAAAATAAT
1 AAAAATAATAAAAATAAATATATATATATAAAATAAT
111035 AAAAA-AAGTAAAAAT-AATATATATATATAAAATAA-
1 AAAAATAA-TAAAAATAAATATATATATATAAAATAAT
111070 AAAAATAA-AAAAAGTAAATATATATATATATAAATTAAT
1 AAAAATAATAAAAA-TAAATATATATATATA-AAA-TAAT
* * *
111109 AAAACTGATAATAAAAAATAATATATTTATATATATAAT-CT
1 AAAA---ATAAT-AAAAATAA-ATATATATATATAAAATAAT
111150 AAAAA-AATAAAAATA
1 AAAAATAATAAAAATA
111165 TATACTAAAG
Statistics
Matches: 108, Mismatches: 7, Indels: 29
0.75 0.05 0.20
Matches are distributed among these distances:
34 5 0.05
35 14 0.13
36 43 0.40
37 6 0.06
38 4 0.04
39 4 0.04
41 5 0.05
42 5 0.05
43 5 0.05
44 17 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (37 bp):
AAAAATAATAAAAATAAATATATATATATAAAATAAT
Found at i:111097 original size:42 final size:42
Alignment explanation
Indices: 111023--111162 Score: 146
Period size: 41 Copynumber: 3.4 Consensus size: 42
111013 TAAAACAAAT
* *
111023 AAATAAAATAATAAAAAAAGTAAAAATA-ATATATATATATA
1 AAATAAAAAAATAAAAAAAGTAAATATATATATATATATATA
*
111064 AAATAAAAAAATAAAAAAAGTAAATATATATATATATAAAT-
1 AAATAAAAAAATAAAAAAAGTAAATATATATATATATATATA
* ** *
111105 TAATAAAACTGATAATAAAAAAT-AATATAT-T-TATATATATA
1 AAATAAAA-AAATAA-AAAAAGTAAATATATATATATATATATA
**
111146 ATCTAAAAAAATAAAAA
1 AAATAAAAAAATAAAAA
111163 TATATACTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
39 3 0.04
40 12 0.15
41 39 0.48
42 22 0.27
43 6 0.07
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (42 bp):
AAATAAAAAAATAAAAAAAGTAAATATATATATATATATATA
Found at i:111213 original size:23 final size:22
Alignment explanation
Indices: 111158--111219 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
111148 CTAAAAAAAT
111158 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
111179 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
111202 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
111220 AAAAGAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:111587 original size:34 final size:34
Alignment explanation
Indices: 111544--111612 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
111534 GAATCCTAGC
111544 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
111578 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
111612 A
1 A
111613 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:112377 original size:98 final size:98
Alignment explanation
Indices: 112208--112466 Score: 304
Period size: 98 Copynumber: 2.6 Consensus size: 98
112198 TGGAACCGAA
* * *
112208 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
* * *
112273 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
** * * *
112306 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
112371 ATATCCTCCGCTGTGAAGTTGAAATTGGC-CCTG
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC-G
* * * *
112404 AAACTGGGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAA-T-TG----T-TTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTC
112467 ATAGGTAGCA
Statistics
Matches: 135, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
97 2 0.01
98 87 0.64
99 1 0.01
100 1 0.01
104 1 0.01
105 43 0.32
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (98 bp):
AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
Found at i:112460 original size:105 final size:102
Alignment explanation
Indices: 112208--112600 Score: 334
Period size: 105 Copynumber: 3.8 Consensus size: 102
112198 TGGAACCGAA
* *
112208 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* * ** * ** ** **
112272 A-ATATCCTTCGTTGT-GAAGTTGAG-ATTG-GCTCCG
65 AGATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
** * * * *
112306 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* **
112370 A-ATATCCTCCG-CTGTGAAGTTGAAATTGGCCCTGAAACTGGG
65 AGATATCCTCCGTC-GTG--G--AAAATCAGCCCTGAAA-TGGG
* * *
112412 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCATAGGTAGCA
1 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
** *
112477 TGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATTGG
66 -GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
* **
112515 AAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGG
1 AAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAC
*
112580 CACGATATCCTCCATCGTGGA
64 CA-GATATCCTCCGTCGTGGA
112601 GTTGAAATCG
Statistics
Matches: 238, Mismatches: 42, Indels: 23
0.79 0.14 0.08
Matches are distributed among these distances:
98 68 0.29
101 1 0.00
103 9 0.04
104 18 0.08
105 117 0.49
106 11 0.05
108 13 0.05
109 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (102 bp):
AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
Found at i:113209 original size:67 final size:65
Alignment explanation
Indices: 113077--113469 Score: 268
Period size: 65 Copynumber: 5.8 Consensus size: 65
113067 AGATATCTGA
* * * **
113077 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-T
113142 TT
64 TT
* * *
113144 GTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATT
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
113209 T
65 T
* ** * * **
113210 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-----T-AA-A-TT
* * *
113274 AAAAAACTT
57 CAAAGATTT
* * * * * * * * * *
113283 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTT
* * * **
113348 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTTAAGGGAAA-ATGTCTCAAGATAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAAT-TC---A-A-
*
113412 ACGAAATT
60 A-G-ATTT
* *
113420 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
113470 CTGTCTCAAG
Statistics
Matches: 253, Mismatches: 54, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
64 3 0.01
65 85 0.34
66 8 0.03
67 24 0.09
68 32 0.13
69 1 0.00
70 2 0.01
71 2 0.01
72 54 0.21
73 42 0.17
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTT
Found at i:113260 original size:36 final size:35
Alignment explanation
Indices: 113209--113489 Score: 254
Period size: 36 Copynumber: 8.0 Consensus size: 35
113199 TTCAAAGATT
* *
113209 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
113245 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
113280 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
113318 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
113347 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * *
113382 TTTATTTTAAGGGAAAATGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
113419 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
113454 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
113490 CTCTTCTAGT
Statistics
Matches: 199, Mismatches: 30, Indels: 32
0.76 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 10 0.05
36 129 0.65
37 32 0.16
38 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:113318 original size:138 final size:137
Alignment explanation
Indices: 113160--113470 Score: 417
Period size: 138 Copynumber: 2.3 Consensus size: 137
113150 CAAGAGTAAT
* * *
113160 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * *
113225 TGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCC
66 TGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGAAAAAA-TTAGTTCC
113289 AAAAGAAAC
129 AAAAGAAAC
* * * * *
113298 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * ** * *
113363 TGTCTCAAGAGAGACAAAATTTATTTTAAGGGAAAATGTCTCAAGATAGACGAAATTTGTTTCAA
66 TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGAAAAAATTAGTTCCAA
*
113428 GAGAAAC
131 AAGAAAC
*
113435 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
113471 TGTCTCAAGA
Statistics
Matches: 149, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 50 0.34
138 99 0.66
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (137 bp):
TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGAAAAAATTAGTTCCAA
AAGAAAC
Found at i:113433 original size:102 final size:102
Alignment explanation
Indices: 113245--113433 Score: 272
Period size: 102 Copynumber: 1.9 Consensus size: 102
113235 TAGACGAAAA
* *
113245 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAGA
113310 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
* * * ** ** *
113347 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTTAAGGGAAAATGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAGA
113411 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
113434 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
101 35 0.46
102 41 0.54
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
Found at i:113511 original size:35 final size:36
Alignment explanation
Indices: 113351--113523 Score: 156
Period size: 36 Copynumber: 4.8 Consensus size: 36
113341 AATATTTTGT
* * **
113351 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
113387 TTTAAGGGAAAA-TGTCTCAAGATAGACGAAATTTGT
1 TTCAA-GGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
113423 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
113459 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
113493 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
113524 TCTTGTTTTA
Statistics
Matches: 117, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
34 7 0.06
35 25 0.21
36 79 0.68
37 6 0.05
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:113530 original size:71 final size:72
Alignment explanation
Indices: 113351--113531 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 72
113341 AATATTTTGT
* * * *
113351 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTTAAGGGAAAATGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGACGA
** *
113416 AATTTGT
66 AAACTGC
*
113423 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGACGA
113487 AAACT-C
66 AAACTGC
* * * *
113493 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
113532 TAAGAAAAAC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
70 10 0.11
71 27 0.28
72 58 0.61
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGACGA
AAACTGC
Found at i:113995 original size:18 final size:18
Alignment explanation
Indices: 113968--114003 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
113958 TGTTGAATCC
* *
113968 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
113986 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
114004 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:114445 original size:22 final size:22
Alignment explanation
Indices: 114419--114473 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
114409 TTGTGTTTGG
114419 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
114441 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
114463 TCAAAGGTTTG
1 TCAAAGGTTTG
114474 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:115134 original size:19 final size:18
Alignment explanation
Indices: 115110--115161 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 18
115100 TCCCTTTTTC
115110 TTTTTGATTTTTGCTCTTT
1 TTTTTG-TTTTTGCTCTTT
*
115129 TTTTTGTTCTTGTTTCTCTTT
1 TTTTTG-T-TT-TTGCTCTTT
115150 TTCTTTGTTTTT
1 TT-TTTGTTTTT
115162 TTTTTGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 11 0.39
22 4 0.14
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.77
Consensus pattern (18 bp):
TTTTTGTTTTTGCTCTTT
Found at i:115171 original size:22 final size:23
Alignment explanation
Indices: 115117--115173 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
115107 TTCTTTTTGA
*
115117 TTTTTGCTCTTTTTTTTGTTCTTG
1 TTTTTGCT-TTTTCTTTGTTCTTG
* *
115141 TTTCT-CTTTTTCTTTGTT-TTT
1 TTTTTGCTTTTTCTTTGTTCTTG
115162 TTTTTGCTTTTT
1 TTTTTGCTTTTT
115174 TGCTTCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 2 0.07
24 4 0.14
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (23 bp):
TTTTTGCTTTTTCTTTGTTCTTG
Found at i:115187 original size:16 final size:16
Alignment explanation
Indices: 115145--115196 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
115135 TTCTTGTTTC
*
115145 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
*
115161 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
115178 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
115193 TCTT
1 TCTT
115197 GATTGGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:116322 original size:8 final size:8
Alignment explanation
Indices: 116306--116344 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
116296 AATGTAGATG
116306 AAAATGCA
1 AAAATGCA
*
116314 AAAAGGCA
1 AAAATGCA
116322 AAAATGC-
1 AAAATGCA
116329 AAAATGCA
1 AAAATGCA
*
116337 AGAATGCA
1 AAAATGCA
116345 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:116332 original size:15 final size:15
Alignment explanation
Indices: 116306--116344 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
116296 AATGTAGATG
116306 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
116322 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
116337 AGAATGCA
1 AAAATGCA
116345 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:118795 original size:15 final size:15
Alignment explanation
Indices: 118777--118806 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
118767 AAAACCATGT
118777 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
118792 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
118807 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:118813 original size:15 final size:15
Alignment explanation
Indices: 118780--118814 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
118770 ACCATGTTAG
* *
118780 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
118795 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
118810 ATAAA
1 ATAAA
118815 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:118937 original size:8 final size:9
Alignment explanation
Indices: 118913--118938 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
118903 ATAAAAAATA
118913 AAGAAAAAG
1 AAGAAAAAG
118922 AAGAAAAAG
1 AAGAAAAAG
118931 AAGAAAAA
1 AAGAAAAA
118939 AATATAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:118976 original size:47 final size:49
Alignment explanation
Indices: 118917--119022 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 49
118907 AAAATAAAGA
* *
118917 AAAAGAAG-AAAAAGAAG-AAAAA-AATATAGAAATAAAAC-AAATAAAT
1 AAAATAAGTAAAAA-AAGTAAAAATAATATAGAAATAAAACAAAAAAAAT
* * *
118963 AAAATAA-TAAAAAAAGTAAAAATAATATATATATATAACAAAAAAAAT
1 AAAATAAGTAAAAAAAGTAAAAATAATATAGAAATAAAACAAAAAAAAT
119011 AAAATAAGTAAA
1 AAAATAAGTAAA
119023 TATATATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
45 3 0.06
46 16 0.32
47 13 0.26
48 14 0.28
49 4 0.08
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (49 bp):
AAAATAAGTAAAAAAAGTAAAAATAATATAGAAATAAAACAAAAAAAAT
Found at i:119090 original size:35 final size:35
Alignment explanation
Indices: 118970--119099 Score: 110
Period size: 35 Copynumber: 3.6 Consensus size: 35
118960 AATAAAATAA
*
118970 TAAAAAAAGT-AAAAATA-ATATATATATATAA-C
1 TAAAAAAAATAAAAAATATATATATATATATAATC
*
119002 -AAAAAAAATAAAATAAGTAAATATATATATATAAAT-
1 TAAAAAAAATAAAA-AA-TATATATATATATAT-AATC
*
119038 TAATAAAACTGATAATAAAAAATATATTTATATATATAATC
1 T-A-AAAA---A-AATAAAAAATATATATATATATATAATC
119079 TAAAAAAAAT-AAAAATATATA
1 TAAAAAAAATAAAAAATATATA
119100 CTAAAGTAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 26
0.73 0.04 0.24
Matches are distributed among these distances:
31 8 0.10
32 3 0.04
33 2 0.03
34 12 0.15
35 15 0.19
36 3 0.04
38 1 0.01
39 8 0.10
40 4 0.05
41 14 0.17
42 3 0.04
43 7 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (35 bp):
TAAAAAAAATAAAAAATATATATATATATATAATC
Found at i:119143 original size:22 final size:21
Alignment explanation
Indices: 119089--119149 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
119079 TAAAAAAAAT
119089 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
119109 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
119132 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
119150 AAAAAGAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 10 0.31
23 12 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:119518 original size:34 final size:34
Alignment explanation
Indices: 119475--119543 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
119465 GAATCCTAGC
119475 AAAATTCTATCATATCTTTAGAAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGAAGTTTGAATCCT
* * *
119509 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGAAGTTTGAATCCT
119543 A
1 A
119544 CTAGGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGAAGTTTGAATCCT
Found at i:125316 original size:28 final size:28
Alignment explanation
Indices: 125275--125333 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
125265 TACATTTCAA
*
125275 TTTTTAATAAAAAATTAAATTCAAATAT
1 TTTTTAATAAAAAATTAAATTAAAATAT
*
125303 TTTTTAA-AATAAAATTAAATTAAAATCT
1 TTTTTAATAA-AAAATTAAATTAAAATAT
125331 TTT
1 TTT
125334 ATTCACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTTAATAAAAAATTAAATTAAAATAT
Found at i:126165 original size:186 final size:187
Alignment explanation
Indices: 125840--126219 Score: 638
Period size: 186 Copynumber: 2.0 Consensus size: 187
125830 AATCAAAATC
* * * *
125840 AAATTTTAAATATATTATATATATAACATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAAT
1 AAATATTAAATATATTATATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAAT
125905 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
66 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
* *
125970 TTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAA
131 TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTT-AATTAAA
*
126028 AAATATTAAATATA-T-TATATATAACATATGGACTCAACCCAAACTATTTAAAACCCAATTAAT
1 AAATATTAAATATATTATATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAAT
* * **
126091 AATTTAATATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAAAAT
66 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
126156 TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTAATTAAA
131 TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTAATTAAA
126213 AAATATT
1 AAATATT
126220 TAATTTTTTT
Statistics
Matches: 181, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
185 14 0.08
186 153 0.85
187 1 0.01
188 13 0.07
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (187 bp):
AAATATTAAATATATTATATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAAT
AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTAATTAAA
Found at i:128932 original size:18 final size:18
Alignment explanation
Indices: 128896--128933 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
128886 TGACATGGTG
*
128896 TTGCAACTAACATTATTT
1 TTGCAACTAACAATATTT
128914 TTGCAACATAACAAT-TTT
1 TTGCAAC-TAACAATATTT
128932 TT
1 TT
128934 CCATAATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (18 bp):
TTGCAACTAACAATATTT
Found at i:137266 original size:2 final size:2
Alignment explanation
Indices: 137259--137293 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
137249 AAGAAAACAA
137259 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
137294 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:137298 original size:2 final size:2
Alignment explanation
Indices: 137293--137322 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
137283 TCTCTCTCTC
137293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137323 GTCAATTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141739 original size:28 final size:28
Alignment explanation
Indices: 141707--141809 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
141697 AGAATTTGTA
* *
141707 CCGAATGACCACATAAAACACATATGTC
1 CCGAAGGACCACATAGAACACATATGTC
*
141735 CCGAAGGACCACATAGAACATATATGTC
1 CCGAAGGACCACATAGAACACATATGTC
141763 CCGAAGGACCACATAGAACACATATGTC
1 CCGAAGGACCACATAGAACACATATGTC
* *
141791 CCGAAGGACTACGTAGAAC
1 CCGAAGGACCACATAGAAC
141810 CCTCGACTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.16
Consensus pattern (28 bp):
CCGAAGGACCACATAGAACACATATGTC
Found at i:144583 original size:3 final size:3
Alignment explanation
Indices: 144575--144612 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
144565 TTACCAAAAA
144575 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
144613 GTAGTAGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:144617 original size:3 final size:3
Alignment explanation
Indices: 144611--144641 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
144601 TTATTATTAT
144611 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
144642 TGACAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:148374 original size:13 final size:13
Alignment explanation
Indices: 148354--148386 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
148344 CATCTCCATC
*
148354 TTTT-TTTCTTTA
1 TTTTCTTTCATTA
148366 TTTTCTTTCATTA
1 TTTTCTTTCATTA
148379 TTTTCTTT
1 TTTTCTTT
148387 TCACAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:149010 original size:14 final size:14
Alignment explanation
Indices: 148956--149020 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
148946 ATTCTTCTAC
148956 TTTATTTA-TTTTA
1 TTTATTTATTTTTA
*
148969 -TTA-TTATTATT-
1 TTTATTTATTTTTA
* *
148980 TTTATTCAATATTTA
1 TTTATT-TATTTTTA
148995 TTTATTTATTTTTA
1 TTTATTTATTTTTA
*
149009 TTCATTTATTTT
1 TTTATTTATTTT
149021 CATTAGTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
11 3 0.08
12 9 0.22
13 1 0.03
14 21 0.52
15 6 0.15
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:163247 original size:2 final size:2
Alignment explanation
Indices: 163240--163274 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
163230 CTAGGAGCAA
163240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163275 TATTTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:165670 original size:3 final size:3
Alignment explanation
Indices: 165656--165727 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
165646 CCATTTTTAT
* * *
165656 TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
165704 -TA ATA TATA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
165728 AAAAAATAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:165682 original size:15 final size:15
Alignment explanation
Indices: 165664--165727 Score: 103
Period size: 15 Copynumber: 4.3 Consensus size: 15
165654 ATTTATTATA
165664 ATTATTATTATAATT
1 ATTATTATTATAATT
165679 ATTATTATTATAATT
1 ATTATTATTATAATT
165694 ATTATTATTATAA-T
1 ATTATTATTATAATT
*
165708 ATATATTATTATTATT
1 AT-TATTATTATAATT
165724 ATTA
1 ATTA
165728 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
14 3 0.07
15 40 0.87
16 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATTATAATT
Found at i:167399 original size:23 final size:26
Alignment explanation
Indices: 167367--167416 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
167357 CCTTTTCTGA
*
167367 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
167390 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
167416 T
1 T
167417 TTAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:171256 original size:15 final size:15
Alignment explanation
Indices: 171236--171267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
171226 ATCAATACCT
171236 TTTTGCATACATACA
1 TTTTGCATACATACA
*
171251 TTTTGCATACATTCA
1 TTTTGCATACATACA
171266 TT
1 TT
171268 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:180290 original size:115 final size:115
Alignment explanation
Indices: 179994--180458 Score: 791
Period size: 115 Copynumber: 4.1 Consensus size: 115
179984 TAATTGGAAC
179994 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
180059 TTATCTGATCTGGTTTGGTATGAAACCCAAAAACCAATCATTGGA----A
66 TTATCTGATCTGGTTTGGTATGAAACCCAAAAACCAATCATTGGATTTGA
*
180105 CAAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGA
1 -AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGA
180170 GTTATCTGATCTGGTTTGGTATGAAACCCAAAAACCAATCATTGGATTTGA
65 GTTATCTGATCTGGTTTGGTATGAAACCCAAAAACCAATCATTGGATTTGA
180221 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
*
180286 TTATCTGATCTGGTTTGGTATG-AACCCTAAAAATCAATCATTGGATTTGA
66 TTATCTGATCTGGTTTGGTATGAAACCC-AAAAACCAATCATTGGATTTGA
180336 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
* * * * *
180401 TTATCTGATCTGGTTCGGTA-GGAA-CCACAGAACCAATCATTGGAATTAA
66 TTATCTGATCTGGTTTGGTATGAAACCCA-AAAACCAATCATTGGATTTGA
180450 AAGATGAAT
1 AAGATGAAT
180459 TGCATGATCG
Statistics
Matches: 338, Mismatches: 8, Indels: 12
0.94 0.02 0.03
Matches are distributed among these distances:
112 109 0.32
113 1 0.00
114 34 0.10
115 193 0.57
116 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (115 bp):
AAGATGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
TTATCTGATCTGGTTTGGTATGAAACCCAAAAACCAATCATTGGATTTGA
Found at i:181391 original size:113 final size:113
Alignment explanation
Indices: 181146--181887 Score: 1061
Period size: 113 Copynumber: 6.6 Consensus size: 113
181136 GCAAAGATTC
* * * * ****
181146 AAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
181211 AAGGAGGTAG-AGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACT-TTTTGCTA
* *
181258 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
181323 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
66 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
*
181371 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
181436 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
66 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
* *
181484 AAATCCATCACTTGATGGATCAGCATTACTAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
181549 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
66 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
*
181597 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
181662 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
* * * * * * * *
181710 AAATTCACCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTG
* * *
181775 AAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
63 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
* * *
181822 AAATCCATCACTTGAT-GATCAGCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCATTACCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
181884 GAAG
65 GAAG
181888 AAGTTCACAA
Statistics
Matches: 586, Mismatches: 37, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
107 12 0.02
108 1 0.00
109 2 0.00
110 18 0.03
111 11 0.02
112 112 0.19
113 411 0.70
114 2 0.00
115 5 0.01
116 12 0.02
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTA
Found at i:181978 original size:339 final size:332
Alignment explanation
Indices: 181146--182042 Score: 940
Period size: 339 Copynumber: 2.7 Consensus size: 332
181136 GCAAAGATTC
* * * * *
181146 AAATCCATCATTTGATGGATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCATTACCAGTAG--AGTTCATAATAAGAAGAACTCATCT--A
* * * * * *** *
181210 GAAGGAGGTAGAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCAAATCCATCACTTGATG
62 GAA-GAAG-A-AGTTCACAATAAGAAGAACTTGTTCAACCTTTTGCTAAAATCCATCAAGAGATA
* **
181275 GATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
124 GATCAGCATAACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
181340 TAATAAGAAGAACTTGTTCAACTTTTTGCTAAAATCCATCACTTGATGGATCAGCATTACCAGTT
189 TAATGAGAAGAACTTGTTCAACTTTTTGCTAAAATCCACCACTTGATGGATCAACATTACCAGGT
*
181405 CGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
254 AGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
181470 TCAACTTTTTGCTA
319 TCAACTTTTTGCTA
* *
181484 AAATCCATCACTTGATGGATCAGCATTACTAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCATTACCAG-TAGAGTTCATAATAAGAAGAACTCATCT----
* * *** *
181549 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCTAAAATCCATCACTTGATG
61 -A-GAAGAAGAAGTTCACAATAAGAAGAACTTGTTCAACCTTTTGCTAAAATCCATCAAGAGATA
* *
181614 GATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
124 GATCAGCATAACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * * *
181679 TAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCACCATTTGATGGATTAACATTGCCAGGT
189 TAATGAGAAGAACTTGTTCAACTTTTTGCTAAAATCCACCACTTGATGGATCAACATTACCAGGT
* * *
181744 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATT
254 AGAGTTCATAATAAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACT
*
181805 TGTTCAACTTTTTGCTC
316 TGTTCAACTTTTTGCTA
* * *
181822 AAATCCATCACTTGAT-GATCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCT-GAA
1 AAATCCATCACTTGATGGATCAGCATTACCAGTAG-AGTTCATAATAAGAAGAACTCATCTAGAA
* * * *
181884 GAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC-ATAATTCTATTACAGAAAGAGATA
65 GAAGAAGTTCACAATAAGAAGAACTTGTTCAACCTTTTGCTA-AAATCCA-T-C---AAGAGATA
* *
181948 GATTAGCATCAACC-TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGA
124 GATCAGCAT-AACCAGTT-C---G-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
182008 AGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
183 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
182043 ATAATTCTAT
Statistics
Matches: 484, Mismatches: 53, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
328 1 0.00
329 44 0.09
330 1 0.00
331 1 0.00
334 14 0.03
335 44 0.09
336 27 0.06
337 12 0.02
338 100 0.21
339 211 0.44
340 3 0.01
341 11 0.02
342 15 0.03
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (332 bp):
AAATCCATCACTTGATGGATCAGCATTACCAGTAGAGTTCATAATAAGAAGAACTCATCTAGAAG
AAGAAGTTCACAATAAGAAGAACTTGTTCAACCTTTTGCTAAAATCCATCAAGAGATAGATCAGC
ATAACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACTTTTTGCTAAAATCCACCACTTGATGGATCAACATTACCAGGTAGAGTTC
ATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTT
TTTGCTA
Found at i:182021 original size:223 final size:231
Alignment explanation
Indices: 181746--182240 Score: 553
Period size: 239 Copynumber: 2.1 Consensus size: 231
181736 TGCCAGGTAG
* *
181746 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCA
* * * * *
181811 ACTTTTTGC-TCAAATCCA-T-C-A-CTTGA-T-G-ATCAGCTTTTCCAGAG-AAGTTCATAATG
63 ACCTTTTGCAT-AAATCCATTACAAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATG
* * *
181867 AGAAGAACTCATCT-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTC
127 AGAAGAACTCATCTAGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGAATAACTC
* * * * **
181931 TATTACAGAAAGAGATAGATTAGCATCA-ACCTTTCCAGAGA
192 TATCACAGAAAGAAATAGATCAACATCATACCCAT-CAGA-A
* *
181972 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACC
* *
182037 TTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAAT
66 TTTTGCATAAATCCATTAC----A-AGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAAT
*
182102 GAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGAATGA
126 GAGAAGAACTCATCT--AGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGAATAA
* * * * *
182167 CTCTATCACAGAAGGAAATAGGTCAACTTCATCCCCATCGGAA
189 CTCTATCACAGAAAGAAATAGATCAACATCATACCCATCAGAA
*
182210 AGTTCATAATGAGAAAAACTCATCTGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA
182241 AGAGAAGAAT
Statistics
Matches: 224, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
223 52 0.23
224 3 0.01
225 1 0.00
226 18 0.08
231 1 0.00
232 3 0.01
233 1 0.00
234 1 0.00
235 14 0.06
236 26 0.12
238 31 0.14
239 70 0.31
240 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (231 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACC
TTTTGCATAAATCCATTACAAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAA
GAACTCATCTAGAAGAAGAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATC
ACAGAAAGAAATAGATCAACATCATACCCATCAGAA
Found at i:182054 original size:119 final size:119
Alignment explanation
Indices: 181846--182240 Score: 593
Period size: 120 Copynumber: 3.3 Consensus size: 119
181836 ATGATCAGCT
181846 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCT---GAAGAAGAAGTTCACAATGAGAAGAGC
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGC
181908 TTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
66 TTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
181962 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGC
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGC
182027 TTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
66 TTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
182081 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAG
1 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAG
* * * * * * * * * * * *
182146 CTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACTTCATCCC
65 CTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCA-ACC
** * *
182202 CAT-CGGA-AAGTTCATAATGAGAAAAACTCATCTGAAGAA
1 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
182241 AGAGAAGAAT
Statistics
Matches: 258, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
116 35 0.14
118 31 0.12
119 90 0.35
120 99 0.38
121 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (119 bp):
TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGC
TTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGCATCAACC
Found at i:182400 original size:3 final size:3
Alignment explanation
Indices: 182392--182448 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
182382 CCATTTTTAT
* *
182392 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA -TA ATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
182437 TTA TTA TTA TTA
1 TTA TTA TTA TTA
182449 AAAAAATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Done.