Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold44
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: 3265628
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28
Warning! 491382 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:538140 original size:126 final size:126
Alignment explanation
Indices: 537995--538224 Score: 406
Period size: 126 Copynumber: 1.8 Consensus size: 126
537985 CTCATTCATG
* *
537995 TAATTCAATAGATTTGAATAGAAAAAATATCTTAAGAGTTTCTTTACTTTTGTGAGAATTTCTTC
1 TAATTCAATAGATTTGAATAGAAAAAATATCTTAAGAGTTTCTTCACTTTTGTGAGAACTTCTTC
538060 TTTGTTCTTTAAACAAGAACTCAAATTGATCTTATCAAGATAACTTTTAGCGATCAAAATT
66 TTTGTTCTTTAAACAAGAACTCAAATTGATCTTATCAAGATAACTTTTAGCGATCAAAATT
* * *
538121 TAATTCAGTAGATTTGAATAGAAAAAATATCTTGAGAGTTTCTTCATTTTTGTGAGAACTTCTTC
1 TAATTCAATAGATTTGAATAGAAAAAATATCTTAAGAGTTTCTTCACTTTTGTGAGAACTTCTTC
*
538186 TTTGTTCTTTAAACAAGAACTTAAATTGATCTTATCAAG
66 TTTGTTCTTTAAACAAGAACTCAAATTGATCTTATCAAG
538225 GTAATTGTGG
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 98 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (126 bp):
TAATTCAATAGATTTGAATAGAAAAAATATCTTAAGAGTTTCTTCACTTTTGTGAGAACTTCTTC
TTTGTTCTTTAAACAAGAACTCAAATTGATCTTATCAAGATAACTTTTAGCGATCAAAATT
Found at i:539188 original size:13 final size:13
Alignment explanation
Indices: 539148--539199 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
539138 CTGTTACAAG
539148 CAATGTATCGATA
1 CAATGTATCGATA
539161 CAA--T-TC-AT-
1 CAATGTATCGATA
539169 C-ATGTATCGATA
1 CAATGTATCGATA
539181 CAATGTATCGATA
1 CAATGTATCGATA
*
539194 TAATGT
1 CAATGT
539200 GCCATGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:539188 original size:33 final size:33
Alignment explanation
Indices: 539148--539215 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
539138 CTGTTACAAG
539148 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
*
539181 CAATGTATCGATATAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
539214 CA
1 CA
539216 TTGATTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:539260 original size:105 final size:105
Alignment explanation
Indices: 539098--539321 Score: 448
Period size: 105 Copynumber: 2.1 Consensus size: 105
539088 ACAATTCATA
539098 ATGTATCGATACATTGATTTGAAATTATAGTCGTTTATAGCTGTTACAAGCAATGTATCGATACA
1 ATGTATCGATACATTGATTTGAAATTATAGTCGTTTATAGCTGTTACAAGCAATGTATCGATACA
539163 ATTCATCATGTATCGATACAATGTATCGATATAATGTGCC
66 ATTCATCATGTATCGATACAATGTATCGATATAATGTGCC
539203 ATGTATCGATACATTGATTTGAAATTATAGTCGTTTATAGCTGTTACAAGCAATGTATCGATACA
1 ATGTATCGATACATTGATTTGAAATTATAGTCGTTTATAGCTGTTACAAGCAATGTATCGATACA
539268 ATTCATCATGTATCGATACAATGTATCGATATAATGTGCC
66 ATTCATCATGTATCGATACAATGTATCGATATAATGTGCC
539308 ATGTATCGATACAT
1 ATGTATCGATACAT
539322 ACAGTGGTAG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (105 bp):
ATGTATCGATACATTGATTTGAAATTATAGTCGTTTATAGCTGTTACAAGCAATGTATCGATACA
ATTCATCATGTATCGATACAATGTATCGATATAATGTGCC
Found at i:539293 original size:13 final size:13
Alignment explanation
Indices: 539253--539304 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
539243 CTGTTACAAG
539253 CAATGTATCGATA
1 CAATGTATCGATA
539266 CAA--T-TC-AT-
1 CAATGTATCGATA
539274 C-ATGTATCGATA
1 CAATGTATCGATA
539286 CAATGTATCGATA
1 CAATGTATCGATA
*
539299 TAATGT
1 CAATGT
539305 GCCATGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:539293 original size:33 final size:33
Alignment explanation
Indices: 539253--539320 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
539243 CTGTTACAAG
539253 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
*
539286 CAATGTATCGATATAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
539319 CA
1 CA
539321 TACAGTGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:539394 original size:19 final size:18
Alignment explanation
Indices: 539349--539406 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
539339 ACTGCCAGTT
539349 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
539368 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
539387 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
539406 T
1 T
539407 ATCGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:539408 original size:13 final size:13
Alignment explanation
Indices: 539390--539421 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
539380 TACAATGATC
539390 ATGTATCGATACA
1 ATGTATCGATACA
539403 ATGTATCGATACA
1 ATGTATCGATACA
*
539416 AAGTAT
1 ATGTAT
539422 AATGTATCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:539412 original size:32 final size:33
Alignment explanation
Indices: 539371--539435 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
539361 ACAATTGTCC
* *
539371 ATGTATCGATACAATG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGTATAATGTATCGATACA
*
539403 ATGTATCGATACAAAGTATAATGTATCGGTACA
1 ATGTATCGATACAAAGTATAATGTATCGATACA
539436 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGTATAATGTATCGATACA
Found at i:541961 original size:13 final size:13
Alignment explanation
Indices: 541943--541969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
541933 ATAGTAACCC
541943 ATGTATCGATACA
1 ATGTATCGATACA
541956 ATGTATCGATACA
1 ATGTATCGATACA
541969 A
1 A
541970 GGAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:545891 original size:21 final size:21
Alignment explanation
Indices: 545860--545907 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
545850 ATGAATCATG
*
545860 CAATTTTTTATTTTTC-TTAGC
1 CAATTTATTA-TTTTCATTAGC
*
545881 TAATTTATTATTTTCATTAGC
1 CAATTTATTATTTTCATTAGC
545902 CAATTT
1 CAATTT
545908 TTTAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.58
Consensus pattern (21 bp):
CAATTTATTATTTTCATTAGC
Found at i:548158 original size:33 final size:33
Alignment explanation
Indices: 548116--548184 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
548106 CCGTTACAAG
* *
548116 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATATATCGATACAATGT-ACCATGTATCGATA
*
548149 CAATATATCGATATAATGTACCATGTATCGATA
1 CAATATATCGATACAATGTACCATGTATCGATA
548182 CAA
1 CAA
548185 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATATATCGATACAATGTACCATGTATCGATA
Found at i:548238 original size:20 final size:20
Alignment explanation
Indices: 548212--548267 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
548202 ATTGCCAGTT
548212 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAATTGA
548231 TCCATGTATCGATACAA-TGA
1 T-CATGTATCGATACAATTGA
548251 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
548268 ATATCGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:548295 original size:33 final size:32
Alignment explanation
Indices: 548237--548298 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
548227 ATTGTCCATG
* *
548237 TATCGATACAATGATCATGTATCGATACAATA
1 TATCGATACAAAGATAATGTATCGATACAATA
548269 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAG-ATAATGTATCGATACA
548299 TCTGGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (32 bp):
TATCGATACAAAGATAATGTATCGATACAATA
Found at i:548979 original size:20 final size:20
Alignment explanation
Indices: 548926--548982 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
548916 TTAGTATCAA
* *
548926 TACAATGTATCGATACATGT
1 TACATTGTATCGATACATCT
* *
548946 T-CATTATATTGATACATCT
1 TACATTGTATCGATACATCT
548965 TACATTGTATCGATACAT
1 TACATTGTATCGATACAT
548983 AAAATTGGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (20 bp):
TACATTGTATCGATACATCT
Found at i:549050 original size:14 final size:14
Alignment explanation
Indices: 549031--549089 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
549021 ATTACTATTC
*
549031 ATCACTGTTCACAT
1 ATCACTGTTCACGT
**
549045 ATCACTGTTCGTGT
1 ATCACTGTTCACGT
* *
549059 ATCATTATTCACGT
1 ATCACTGTTCACGT
*
549073 ATCACTGTTCATGT
1 ATCACTGTTCACGT
549087 ATC
1 ATC
549090 GATATAGTGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (14 bp):
ATCACTGTTCACGT
Found at i:549062 original size:28 final size:28
Alignment explanation
Indices: 549031--549089 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
549021 ATTACTATTC
* *
549031 ATCACTGTTCACATATCACTGTTCGTGT
1 ATCACTATTCACATATCACTGTTCATGT
* *
549059 ATCATTATTCACGTATCACTGTTCATGT
1 ATCACTATTCACATATCACTGTTCATGT
549087 ATC
1 ATC
549090 GATATAGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (28 bp):
ATCACTATTCACATATCACTGTTCATGT
Found at i:549884 original size:2 final size:2
Alignment explanation
Indices: 549877--549904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
549867 TGAGCTAACA
549877 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
549905 CAAAGAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550125 original size:24 final size:26
Alignment explanation
Indices: 550089--550154 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
550079 AGTATATATA
*
550089 AATATTATA-TATAAATTATGTTTAT
1 AATATTAAATTATAAATTATGTTTAT
*
550114 AA-A-TAAATTATAACA-TATTTTTAT
1 AATATTAAATTATAA-ATTATGTTTAT
*
550138 AATATTAAATTAAAAAT
1 AATATTAAATTATAAAT
550155 AATTAGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.09
24 16 0.48
25 5 0.15
26 9 0.27
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
AATATTAAATTATAAATTATGTTTAT
Found at i:550399 original size:13 final size:13
Alignment explanation
Indices: 550381--550407 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
550371 TATTTATTTT
550381 TCAATTTTTTAAC
1 TCAATTTTTTAAC
550394 TCAATTTTTTAAC
1 TCAATTTTTTAAC
550407 T
1 T
550408 ATAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TCAATTTTTTAAC
Found at i:553352 original size:17 final size:17
Alignment explanation
Indices: 553330--553363 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
553320 ATTTTAAGTG
553330 CTTATTAGAATATTATT
1 CTTATTAGAATATTATT
* *
553347 CTTATTATATTATTATT
1 CTTATTAGAATATTATT
553364 ATTTTAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
CTTATTAGAATATTATT
Found at i:555654 original size:4 final size:4
Alignment explanation
Indices: 555645--555671 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
555635 ACATCTCATT
555645 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
555672 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:555699 original size:10 final size:9
Alignment explanation
Indices: 555668--555697 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
555658 ATAAATAAAT
555668 AAATTTTAA
1 AAATTTTAA
555677 AAATTTTAA
1 AAATTTTAA
555686 AAATTTTAA
1 AAATTTTAA
555695 AAA
1 AAA
555698 ATAATTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATTTTAA
Found at i:556185 original size:13 final size:13
Alignment explanation
Indices: 556167--556192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556157 CATTATTCCA
556167 TGTATCGATACAT
1 TGTATCGATACAT
556180 TGTATCGATACAT
1 TGTATCGATACAT
556193 GGATTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:560317 original size:20 final size:19
Alignment explanation
Indices: 560282--560320 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
560272 ATAAGAAATT
*
560282 AATTTTATATATAAATATA
1 AATTTTATAGATAAATATA
560301 AATTTTAATAGATAAATATA
1 AATTTT-ATAGATAAATATA
560321 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTTTATAGATAAATATA
Found at i:563566 original size:13 final size:13
Alignment explanation
Indices: 563548--563572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
563538 CAAAGATCAG
563548 TGTATCGATACAA
1 TGTATCGATACAA
563561 TGTATCGATACA
1 TGTATCGATACA
563573 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:563650 original size:33 final size:33
Alignment explanation
Indices: 563613--563679 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
563603 AGTAGCTTAA
563613 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
563646 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
563679 A
1 A
563680 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:563653 original size:13 final size:13
Alignment explanation
Indices: 563635--563659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
563625 CAAAAAAATA
563635 TGTATCGATACAT
1 TGTATCGATACAT
563648 TGTATCGATACA
1 TGTATCGATACA
563660 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:564006 original size:6 final size:6
Alignment explanation
Indices: 563992--564030 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
563982 AAACCGATTT
* * *
563992 GAACTC GAACCC GAACCC GAACCC GAACCT GAATCC GAA
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAA
564031 AAAAGCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.38, G:0.18, T:0.08
Consensus pattern (6 bp):
GAACCC
Found at i:564091 original size:16 final size:16
Alignment explanation
Indices: 564072--564106 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
564062 AAAAAGCTTA
564072 AACCCGAATAAGTTCG
1 AACCCGAATAAGTTCG
564088 AACCCGAATAAGTTCG
1 AACCCGAATAAGTTCG
564104 AAC
1 AAC
564107 TCAAAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (16 bp):
AACCCGAATAAGTTCG
Found at i:565547 original size:13 final size:13
Alignment explanation
Indices: 565529--565553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
565519 CATAAAATGT
565529 TGTATCGATACAA
1 TGTATCGATACAA
565542 TGTATCGATACA
1 TGTATCGATACA
565554 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:565551 original size:33 final size:34
Alignment explanation
Indices: 565509--565579 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
565499 TTCAACGATT
565509 TGTATCGATACATA-AAATGTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
*** *
565542 TGTATCGATACATATTTTTTTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
565576 TGTA
1 TGTA
565580 AGCTACTGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (34 bp):
TGTATCGATACATATAAATGTTGTATCGATACAA
Found at i:565694 original size:32 final size:32
Alignment explanation
Indices: 565653--565751 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 32
565643 CACTGATCTT
565653 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
565685 TGTATCGATACAT-------TATTAT---AAAA
1 TGTATCGATACATGCAGGCAAATT-TGCCCAGA
565708 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGA
565740 TGTATCGATACA
1 TGTATCGATACA
565752 CTATTAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 22
0.64 0.08 0.28
Matches are distributed among these distances:
23 15 0.30
25 3 0.06
26 1 0.02
29 1 0.02
30 3 0.06
32 27 0.54
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:565784 original size:52 final size:55
Alignment explanation
Indices: 565653--565776 Score: 218
Period size: 55 Copynumber: 2.3 Consensus size: 55
565643 CACTGATCTT
*
565653 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTATAAAA
565708 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTA-T-T-AAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTATAAAA
565760 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
565777 ATAAATTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
52 20 0.29
53 1 0.01
54 1 0.01
55 46 0.68
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (55 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTATAAAA
Found at i:569592 original size:3 final size:3
Alignment explanation
Indices: 569584--569614 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
569574 ATATATAATT
569584 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
569615 AAAACTAATG
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:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:574351 original size:19 final size:20
Alignment explanation
Indices: 574329--574366 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
574319 TTTGTTTTAG
574329 TATGTTTCATT-TTTTTTTT
1 TATGTTTCATTATTTTTTTT
574348 TATGTTTCATTATTTTTTT
1 TATGTTTCATTATTTTTTT
574367 AAATTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
TATGTTTCATTATTTTTTTT
Found at i:574363 original size:18 final size:19
Alignment explanation
Indices: 574329--574367 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
574319 TTTGTTTTAG
*
574329 TATGTTTCATTTTTTTTTT
1 TATGTTTCATTTATTTTTT
574348 TATGTTTCA-TTATTTTTT
1 TATGTTTCATTTATTTTTT
574366 TA
1 TA
574368 AATTTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TATGTTTCATTTATTTTTT
Found at i:574603 original size:14 final size:15
Alignment explanation
Indices: 574584--574614 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
574574 CTAAGGCTCG
574584 TATTTTTTTAA-AAT
1 TATTTTTTTAATAAT
574598 TATTTTTTTAATAAT
1 TATTTTTTTAATAAT
574613 TA
1 TA
574615 AAAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTTTAATAAT
Found at i:574753 original size:13 final size:13
Alignment explanation
Indices: 574722--574746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
574712 AAAAATAGTT
574722 TTTAAGAAAAATG
1 TTTAAGAAAAATG
574735 TTTAAGAAAAAT
1 TTTAAGAAAAAT
574747 TTGTAAGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TTTAAGAAAAATG
Found at i:575341 original size:19 final size:19
Alignment explanation
Indices: 575317--575361 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
575307 CTTAACACGT
575317 TTCTTTTTCGTTATTT-TTA
1 TTCTTTTTC-TTATTTCTTA
*
575336 TTCTTTTTCTTTTTTCTTA
1 TTCTTTTTCTTATTTCTTA
575355 -TCTTTTT
1 TTCTTTTT
575362 ATAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCTTATTTCTTA
Found at i:576230 original size:15 final size:17
Alignment explanation
Indices: 576188--576231 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
576178 ATTACTGTAA
*
576188 ATAAATATGTATATTTTT
1 ATAAATAT-TAAATTTTT
576206 ATAAATATTAAATTTTT
1 ATAAATATTAAATTTTT
576223 A-AAA-ATTAA
1 ATAAATATTAA
576232 TTTAAGCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 9 0.36
18 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAAATATTAAATTTTT
Found at i:576285 original size:21 final size:20
Alignment explanation
Indices: 576261--576301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
576251 TTGTTTGTAA
* *
576261 AAAGATAGAAGGACAAAAAAG
1 AAAGAAAGAAAGA-AAAAAAG
576282 AAAGAAAGAAAGAAAAAAAG
1 AAAGAAAGAAAGAAAAAAAG
576302 GAAGGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAAAAG
Found at i:578032 original size:13 final size:13
Alignment explanation
Indices: 578014--578052 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
578004 TACACAAAGT
578014 ATGTATCGATACA
1 ATGTATCGATACA
578027 ATGTATCGATACA
1 ATGTATCGATACA
578040 ATGTATCGATACA
1 ATGTATCGATACA
578053 CAAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:582131 original size:15 final size:15
Alignment explanation
Indices: 582111--582141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
582101 TAAAAATGTC
*
582111 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
582126 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
582141 C
1 C
582142 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:584229 original size:13 final size:13
Alignment explanation
Indices: 584211--584249 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
584201 ACATTTTTCT
584211 TTGTATCGATACA
1 TTGTATCGATACA
584224 TTGTATCGATACA
1 TTGTATCGATACA
*
584237 CTGTATCGATACA
1 TTGTATCGATACA
584250 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:586818 original size:13 final size:13
Alignment explanation
Indices: 586800--586825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
586790 TACACAAAGT
586800 ATGTATCGATACA
1 ATGTATCGATACA
586813 ATGTATCGATACA
1 ATGTATCGATACA
586826 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:586823 original size:32 final size:33
Alignment explanation
Indices: 586782--586845 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
586772 TAGCCAAACT
**
586782 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
586814 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
586846 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:587752 original size:20 final size:20
Alignment explanation
Indices: 587727--587780 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
587717 TGCCAGTTTT
**
587727 ATGTATCGATACAATTGTGC
1 ATGTATCGATACAATTGAAC
*
587747 ATGTATTGATACAA-TGAAC
1 ATGTATCGATACAATTGAAC
*
587766 ATATATCGATACAAT
1 ATGTATCGATACAAT
587781 GCATTAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:587825 original size:20 final size:20
Alignment explanation
Indices: 587802--587852 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
587792 AAGCATAATA
587802 TATCGATACATCTGGATGTG
1 TATCGATACATCTGGATGTG
587822 TATCGATACATCTGGATGTG
1 TATCGATACATCTGGATGTG
*
587842 TATCAATACAT
1 TATCGATACAT
587853 ACAAGGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (20 bp):
TATCGATACATCTGGATGTG
Found at i:588068 original size:21 final size:19
Alignment explanation
Indices: 588044--588082 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
588034 TTTAAACGAA
588044 CAAAACTTGTTTACGATTTTT
1 CAAAACTT-TTT-CGATTTTT
*
588065 CAAATCTTTTTCGATTTT
1 CAAAACTTTTTCGATTTT
588083 ATTCAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (19 bp):
CAAAACTTTTTCGATTTTT
Found at i:588833 original size:13 final size:13
Alignment explanation
Indices: 588815--588842 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
588805 CATTATTCAA
588815 TGTATCGATACAT
1 TGTATCGATACAT
588828 TGTATCGATACAT
1 TGTATCGATACAT
588841 TG
1 TG
588843 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:588837 original size:33 final size:33
Alignment explanation
Indices: 588795--588860 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
588785 GCCAAGAAAA
588795 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
588828 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
588861 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:593118 original size:6 final size:6
Alignment explanation
Indices: 593070--593099 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
593060 ACATGATACC
593070 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
593100 TAATCTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:597117 original size:28 final size:28
Alignment explanation
Indices: 597085--597151 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
597075 TAAGGTTTTG
**
597085 TCTTAATAAGACAAAGTGGATAAACTTA
1 TCTTAATAAGACAAAGCAGATAAACTTA
* **
597113 TCTTAATTAGACAAAGCAGATAAGGTTA
1 TCTTAATAAGACAAAGCAGATAAACTTA
597141 TCTTAATAAGA
1 TCTTAATAAGA
597152 TAATGTCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (28 bp):
TCTTAATAAGACAAAGCAGATAAACTTA
Found at i:597213 original size:28 final size:28
Alignment explanation
Indices: 597176--597236 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
597166 TACATATGTT
* *
597176 TAAGATAATATGGATAAGCTTGTCTTAA
1 TAAGAAAATATGGATAAGATTGTCTTAA
597204 TAAGAAAATATGGATAAGATTGTCTTAA
1 TAAGAAAATATGGATAAGATTGTCTTAA
*
597232 CAAGA
1 TAAGA
597237 CAATGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (28 bp):
TAAGAAAATATGGATAAGATTGTCTTAA
Found at i:598630 original size:33 final size:32
Alignment explanation
Indices: 598588--598655 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
598578 CGTTACAAGC
** *
598588 CAATGTATCGATACATTTTATGGTTTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCGATA
598621 CAATGTATCGATACATACTATGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
598653 CAA
1 CAA
598656 GTTTAGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:600651 original size:21 final size:22
Alignment explanation
Indices: 600615--600657 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
600605 GTAGTTACTT
*
600615 AAATTTAGGAATTTGATTTCTA
1 AAATTTAGGAATTTGAATTCTA
*
600637 AAATTTTGGAA-TTGAATTCTA
1 AAATTTAGGAATTTGAATTCTA
600658 GTAGGATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (22 bp):
AAATTTAGGAATTTGAATTCTA
Found at i:609731 original size:159 final size:159
Alignment explanation
Indices: 609451--609742 Score: 575
Period size: 159 Copynumber: 1.8 Consensus size: 159
609441 AAAAATCATA
609451 TTTTAGCCTACAAGTATTGATACATGACATTCATGTATCGATACAAGGTTCCAATGGTTTAAAAT
1 TTTTAGCCTACAAGTATTGATACATGACATTCATGTATCGATACAAGGTTCCAATGGTTTAAAAT
609516 TTCAAAATTCTACAATTTGTATCTATACAACAAGTTAATGCATCGATACATAAGTGAATGTATCG
66 TTCAAAATTCTACAATTTGTATCTATACAACAAGTTAATGCATCGATACATAAGTGAATGTATCG
609581 ATATTTGACCACGTCGAGGCAAAATTTTG
131 ATATTTGACCACGTCGAGGCAAAATTTTG
609610 TTTTAGCCTACAAGTATTGATACATGACATTCATGTATCGATACAAGGTTCCAATGGTTTAAAAT
1 TTTTAGCCTACAAGTATTGATACATGACATTCATGTATCGATACAAGGTTCCAATGGTTTAAAAT
*
609675 TTCAAAATTCTACAATTTGTATCTATACAACAAGTTAATGCATCGATACATAAGTGAATGTATTG
66 TTCAAAATTCTACAATTTGTATCTATACAACAAGTTAATGCATCGATACATAAGTGAATGTATCG
609740 ATA
131 ATA
609743 CATGCTTGCA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 132 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (159 bp):
TTTTAGCCTACAAGTATTGATACATGACATTCATGTATCGATACAAGGTTCCAATGGTTTAAAAT
TTCAAAATTCTACAATTTGTATCTATACAACAAGTTAATGCATCGATACATAAGTGAATGTATCG
ATATTTGACCACGTCGAGGCAAAATTTTG
Found at i:609734 original size:20 final size:20
Alignment explanation
Indices: 609706--609745 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
609696 TCTATACAAC
*
609706 AAGTTAATGCATCGATACAT
1 AAGTGAATGCATCGATACAT
* *
609726 AAGTGAATGTATTGATACAT
1 AAGTGAATGCATCGATACAT
609746 GCTTGCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
AAGTGAATGCATCGATACAT
Found at i:621567 original size:50 final size:51
Alignment explanation
Indices: 621463--621569 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 51
621453 ATTTAATTAG
621463 ATGTATCGATACATTTAGGTCAAAAACCTAGAATGTATCGATAAATGAAGA
1 ATGTATCGATACATTTAGGTCAAAAACCTAGAATGTATCGATAAATGAAGA
* * *
621514 ATGTATCGATGCATTT-GGATC-AAAATCTAGAATGTATCGATACGATGAA-A
1 ATGTATCGATACATTTAGG-TCAAAAACCTAGAATGTATCGATA-AATGAAGA
621564 ATGTAT
1 ATGTAT
621570 TACATTTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
50 29 0.57
51 22 0.43
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACATTTAGGTCAAAAACCTAGAATGTATCGATAAATGAAGA
Found at i:621663 original size:20 final size:20
Alignment explanation
Indices: 621612--621691 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
621602 AACATGATCT
***
621612 TGTATCAATACATTTCAAAAA
1 TGTATCAATACA-TTCACTTA
* *
621633 TGGATCGATACATTCACTTA
1 TGTATCAATACATTCACTTA
621653 TGTATCAATACATTCACTTA
1 TGTATCAATACATTCACTTA
* * *
621673 CGCATCGATACATTCACTT
1 TGTATCAATACATTCACTT
621692 GTTATATCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
20 39 0.80
21 10 0.20
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (20 bp):
TGTATCAATACATTCACTTA
Found at i:622440 original size:53 final size:53
Alignment explanation
Indices: 622287--622476 Score: 181
Period size: 52 Copynumber: 3.6 Consensus size: 53
622277 TGATGAGGAT
* * * * *
622287 GAAAATAGTGCTAATGTGCTGATTCTAGGCTAGCAACATTAGGCTTAATAATG-
1 GAAAA-AGTGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTAAAAATGA
* * * * *
622340 GTAAATGTGCCAATATGCTGATTCAAAGCCAGTAACAATAGGCTTAAAAATGA
1 GAAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTAAAAATGA
* * * *
622393 GAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATT-GGGTTTAAAGT-A
1 GAAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTAAAAATGA
* * *
622444 -AATAAAATGCCAATATGCTAATTCAAGTCCAGC
1 GAA-AAAGTGCCAATATGCTGATTCAAGGCCAGC
622477 GATATCGAAC
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 2 0.02
51 28 0.25
52 46 0.41
53 37 0.33
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (53 bp):
GAAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTAAAAATGA
Found at i:622492 original size:51 final size:52
Alignment explanation
Indices: 622395--622492 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 52
622385 AAAAATGAGA
* * ****
622395 AAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGTTTAAAGTAAAT
1 AAAAGTGCCAATATGCTAATTCAAGGCCAGCGACATCGAACCTAAAGTAAAT
* *
622447 AAAA-TGCCAATATGCTAATTCAAGTCCAGCGATATCGAACCTAAAG
1 AAAAGTGCCAATATGCTAATTCAAGGCCAGCGACATCGAACCTAAAG
622493 AAAGAAGATT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 34 0.89
52 4 0.11
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (52 bp):
AAAAGTGCCAATATGCTAATTCAAGGCCAGCGACATCGAACCTAAAGTAAAT
Found at i:622632 original size:31 final size:31
Alignment explanation
Indices: 622546--622871 Score: 274
Period size: 33 Copynumber: 10.0 Consensus size: 31
622536 GACATTAGGC
* *
622546 TTAGAAGGGTTGCCATCGACTTGTGTGGGCT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCT
* ** *
622577 TTAGTGAAGGGTTACCACTGACTTGTCTGGGCT
1 TTA--GAAGGGTTGCCACCAACTTGTGTGGGCT
* **
622610 TTAGAAGGATTGCCACCAACTTGTGCAGGCT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCT
**
622641 TTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
1 TT--AGAAGGGTTGCCACCAACTTGTGTGGGCT
* *
622674 TTAGAAAATGGGTTGCCACCGACTGGTGTGGGCT
1 TTAG--AA-GGGTTGCCACCAACTTGTGTGGGCT
* * * *
622708 TTTGAAAGGGGTTGCCACTAACTTGAGTGGACT
1 TTAG-AA-GGGTTGCCACCAACTTGTGTGGGCT
* *
622741 TTAGAAGGGTTGCCACCAACTTGTATGGACT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCT
* *
622772 TTAGAAGGGTTGCCACCAACTTATGTGGGTT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCT
* * * *
622803 TTAAAAAAAAGAGGTTGCCACCGACTTGTATAGGCT
1 TT----AGAAG-GGTTGCCACCAACTTGTGTGGGCT
* *
622839 TTAGAGAGGGTTGCCATCGACTTGTGTGGGCT
1 TTAGA-AGGGTTGCCACCAACTTGTGTGGGCT
622871 T
1 T
622872 AAAAAAAAGG
Statistics
Matches: 239, Mismatches: 43, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
31 79 0.33
32 26 0.11
33 83 0.35
34 26 0.11
35 4 0.02
36 21 0.09
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (31 bp):
TTAGAAGGGTTGCCACCAACTTGTGTGGGCT
Found at i:622650 original size:64 final size:64
Alignment explanation
Indices: 622546--622871 Score: 311
Period size: 64 Copynumber: 5.0 Consensus size: 64
622536 GACATTAGGC
* * * * *
622546 TTAGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGTGAAGGGTTACCACTGACTTGTCTGGGCT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
* **
622610 TTAGAAGGATTGCCACCAACTTGTGCAGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
* * * * *
622674 TTAGAAAATGGGTTGCCACCGACTGGTGTGGGCTTTTGA-AAGGGGTTGCCACTAACTTGAGTGG
1 TTAG--AA-GGGTTGCCACCAACTTGTGTGGGCTTTAGAGAA-GGGTTGCCACTGACTTGTGTGG
*
622738 ACT
62 GCT
* * ** * *
622741 TTAGAAGGGTTGCCACCAACTTGTATGGACTTT--AGAAGGGTTGCCACCAACTTATGTGGGTT
1 TTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
* * * *
622803 TTAAAAAAAAGAGGTTGCCACCGACTTGTATAGGCTTTAGAG-AGGGTTGCCA-TCGACTTGTGT
1 TT----AGAAG-GGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACT-GACTTGTGT
622866 GGGCT
60 GGGCT
622871 T
1 T
622872 AAAAAAAAGG
Statistics
Matches: 215, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
62 23 0.11
63 2 0.01
64 83 0.39
65 2 0.01
66 8 0.04
67 73 0.34
68 22 0.10
69 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (64 bp):
TTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCT
Found at i:622819 original size:131 final size:128
Alignment explanation
Indices: 622550--622854 Score: 346
Period size: 131 Copynumber: 2.3 Consensus size: 128
622540 TTAGGCTTAG
* * * * *
622550 AAGGGTTGCCATCGACTTGTGTGGGCTTTAGTG-AAGGGTTACCACTGACTTGTCTGGGCTTTAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT--TGAAAGGGTTGCCACTAACTTGACTGGACTTTAG
** * *
622614 AAGGATTGCCACCAACTTGTGCAGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTAGA
64 AAGGATTGCCACCAACTTGT-CAGGCTTTA-AGAAGGGTTGCCACCAACTTATGTGGGCTTTAAA
622679 AA
127 AA
* * *
622681 ATGGGTTGCCACCGACTGGTGTGGGCTTTTGAAAGGGGTTGCCACTAACTTGAGTGGACTTTAGA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTTGAAA-GGGTTGCCACTAACTTGACTGGACTTTAGA
* *
622746 AGGGTTGCCACCAACTTGT-ATGGACTTT-AGAAGGGTTGCCACCAACTTATGTGGGTTTTAAAA
65 AGGATTGCCACCAACTTGTCA-GG-CTTTAAGAAGGGTTGCCACCAACTTATGTGGGCTTT-AAA
622809 AA
127 AA
* * * *
622811 AAGAGGTTGCCACCGACTTGTATAGGCTTTAGAGAGGGTTGCCA
1 AAG-GGTTGCCACCGACTTGTGTGGGCTTTTGAAAGGGTTGCCA
622855 TCGACTTGTG
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
129 30 0.20
130 19 0.13
131 99 0.67
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (128 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTTGAAAGGGTTGCCACTAACTTGACTGGACTTTAGAA
GGATTGCCACCAACTTGTCAGGCTTTAAGAAGGGTTGCCACCAACTTATGTGGGCTTTAAAAA
Found at i:622886 original size:131 final size:128
Alignment explanation
Indices: 622550--622888 Score: 312
Period size: 131 Copynumber: 2.6 Consensus size: 128
622540 TTAGGCTTAG
* * * * *
622550 AAGGGTTGCCATCGACTTGTGTGGGCTTTAGTGAAGGGTTACCACTGACTTGTCTGGGCTT--TA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG-AGGGTTGCCACTGACTTGTGTGGGCTTAAAA
* ** * *
622613 GAAGGATTGCCACCAACTTGTGCAGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTAG
65 AAAGG--TGCCACCAACTTGT-CAGGCTTTA-AGAAGGGTTGCCACCAACTTATGTGGGCTTTAA
622678 AAA
126 AAA
* * * * * * * * *
622681 ATGGGTTGCCACCGACTGGTGTGGGCTTTTGAAAGGGGTTGCCACTAACTTGAGTGGACTT-TAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGA-GGGTTGCCACTGACTTGTGTGGGCTTAAAA
* *
622745 AAGGGTTGCCACCAACTTGT-ATGGACTTT-AGAAGGGTTGCCACCAACTTATGTGGGTTTTAAA
65 AAAGG-TGCCACCAACTTGTCA-GG-CTTTAAGAAGGGTTGCCACCAACTTATGTGGGCTTT-AA
622808 AAA
126 AAA
* *
622811 AAGAGGTTGCCACCGACTTGTATAGGCTTTAGAGAGGGTTGCCA-TCGACTTGTGTGGGCTTAAA
1 AAG-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACT-GACTTGTGTGGGCTT-AA
622875 AAAAAGGTGCCACC
63 AAAAAGGTGCCACC
622889 GAGTTGTGGA
Statistics
Matches: 167, Mismatches: 32, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
129 29 0.17
130 30 0.18
131 100 0.60
132 8 0.05
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (128 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACTGACTTGTGTGGGCTTAAAAA
AAGGTGCCACCAACTTGTCAGGCTTTAAGAAGGGTTGCCACCAACTTATGTGGGCTTTAAAAA
Found at i:622935 original size:29 final size:28
Alignment explanation
Indices: 622875--622936 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
622865 TGGGCTTAAA
* * * *
622875 AAAAAGGTGCCACCGAGTTGTGGACTTT
1 AAAAAGGTACCACAGAGTTGCGAACTTT
622903 AAAAAGGTACCACAGAGTTGCGAACTTT
1 AAAAAGGTACCACAGAGTTGCGAACTTT
622931 GAAAAA
1 -AAAAA
622937 AAAGGTGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (28 bp):
AAAAAGGTACCACAGAGTTGCGAACTTT
Found at i:622942 original size:60 final size:62
Alignment explanation
Indices: 622872--623028 Score: 210
Period size: 60 Copynumber: 2.5 Consensus size: 62
622862 GTGTGGGCTT
* * *
622872 AAAAAAAAGGTGCCACCGAGTTGTGGACTTTAAAA-AGGTACCACAGAGTTGCGAACTTT-G
1 AAAAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGAGGTACCACAGAGTTACGAACTTTAA
* * * * * *
622932 AAAAAAAAGGTGCTACAGAGTTATGGACTTTAAAAGAGGTGCCATAGAGTTATGGACTTTAA
1 AAAAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGAGGTACCACAGAGTTACGAACTTTAA
622994 AAGAAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
1 AA-AAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
623029 GAAAAAAGTG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 32 0.39
61 19 0.23
62 2 0.02
63 30 0.36
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (62 bp):
AAAAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGAGGTACCACAGAGTTACGAACTTTAA
Found at i:622980 original size:29 final size:29
Alignment explanation
Indices: 622874--623124 Score: 198
Period size: 29 Copynumber: 8.2 Consensus size: 29
622864 GTGGGCTTAA
*
622874 AAAAAAGGTGCCACCGAGTTGTGGACTTT
1 AAAAAAGGTGCCACAGAGTTGTGGACTTT
* * *
622903 -AAAAAGGTACCACAGAGTTGCGAACTTT
1 AAAAAAGGTGCCACAGAGTTGTGGACTTT
* *
622931 GAAAAAAAAGGTGCTACAGAGTTATGGACTTT
1 ---AAAAAAGGTGCCACAGAGTTGTGGACTTT
* * *
622963 AAAAGAGGTGCCATAGAGTTATGGACTTT
1 AAAAAAGGTGCCACAGAGTTGTGGACTTT
622992 AAAAGAAAAAAGGTGCCACAGAGTTGTGGACTTT
1 -----AAAAAAGGTGCCACAGAGTTGTGGACTTT
* * * *
623026 AAAGAAAAAAGTGTCACGGAGTTGTGGACTTC
1 --A-AAAAAGGTGCCACAGAGTTGTGGACTTT
* * ** *
623058 AAAAGAGATGCCATGGAGTTGTAGACTTT
1 AAAAAAGGTGCCACAGAGTTGTGGACTTT
* *
623087 AAAAAAGGTTGCCACAGAGTTATGAACTTT
1 AAAAAAGG-TGCCACAGAGTTGTGGACTTT
623117 GAAAAAAG
1 -AAAAAAG
623125 ATGTCATTGA
Statistics
Matches: 176, Mismatches: 34, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
28 24 0.14
29 53 0.30
30 17 0.10
31 9 0.05
32 47 0.27
34 26 0.15
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (29 bp):
AAAAAAGGTGCCACAGAGTTGTGGACTTT
Found at i:623048 original size:32 final size:34
Alignment explanation
Indices: 622874--623063 Score: 167
Period size: 32 Copynumber: 6.0 Consensus size: 34
622864 GTGGGCTTAA
*
622874 AAAAAAGGTGCCACCGAGTTGTGGACTTT-----
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
* * * *
622903 -AAAAAGGTACCACAGAGTTGCGAACTTT-GAA-
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
* *
622934 AAAAAAGGTGCTACAGAGTTATGGACTTTAAAAG
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
* *
622968 -----AGGTGCCATAGAGTTATGGACTTTAAAAG
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
622997 AAAAAAGGTGCCACAGAGTTGTGGACTTT-AAAG
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
* * *
623030 AAAAAA-GTGTCACGGAGTTGTGGACTTCAAAAG
1 AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
623063 A
1 A
623064 GATGCCATGG
Statistics
Matches: 132, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
28 24 0.18
29 27 0.20
32 42 0.32
33 17 0.13
34 22 0.17
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (34 bp):
AAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAG
Found at i:623125 original size:95 final size:91
Alignment explanation
Indices: 622889--623120 Score: 265
Period size: 95 Copynumber: 2.5 Consensus size: 91
622879 AGGTGCCACC
* * *
622889 GAGTTGTGGACTTT-AAAAAGGTACCACAGAGTTGCGAACTTTGAAA-AAAAAGGTGCTACAGAG
1 GAGTTGTGGACTTTAAAAAAGGTGCCACAGAGTTGTGAACTTTGAAAGAAAAAAGTGCTACAGAG
* *
622952 TTATGGACTTTAAAAGAGGTGCCATA
66 TTATGGACTTCAAAAGAGATGCCATA
* *
622978 GAGTTATGGACTTTAAAAGAAAAAAGGTGCCACAGAGTTGTGGACTTT-AAAGAAAAAAGTG-TC
1 GAGTTGTGGACTTT-----AAAAAAGGTGCCACAGAGTTGTGAACTTTGAAAGAAAAAAGTGCT-
* * *
623041 ACGGAGTTGTGGACTTCAAAAGAGATGCCATG
60 ACAGAGTTATGGACTTCAAAAGAGATGCCATA
* *
623073 GAGTTGTAGACTTTAAAAAAGGTTGCCACAGAGTTATGAACTTTGAAA
1 GAGTTGTGGACTTTAAAAAAGG-TGCCACAGAGTTGTGAACTTTGAAA
623121 AAAGATGTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
89 13 0.11
90 8 0.07
91 19 0.16
92 3 0.03
94 4 0.03
95 72 0.61
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.25
Consensus pattern (91 bp):
GAGTTGTGGACTTTAAAAAAGGTGCCACAGAGTTGTGAACTTTGAAAGAAAAAAGTGCTACAGAG
TTATGGACTTCAAAAGAGATGCCATA
Found at i:630194 original size:20 final size:20
Alignment explanation
Indices: 630147--630201 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
630137 AAAAAAATAG
* *
630147 AATGTATCGATGCATTGAAA
1 AATGTATCGATACATTCAAA
* *
630167 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
*
630187 CATGTATCGATACAT
1 AATGTATCGATACAT
630202 CTGGGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:631584 original size:52 final size:49
Alignment explanation
Indices: 631527--631674 Score: 161
Period size: 51 Copynumber: 2.9 Consensus size: 49
631517 CCCCCGACGA
* * *
631527 GAAAAATTAGTATTTTAGAGATAACAATGGGGCTAGAGTATCCCCGATTAT
1 GAAAAATT-GTGTTTTAGAAATAA-AATGGGGTTAGAGTATCCCCGATTAT
** * *
631578 GGAAAAACGGTGTTTTAAAAAATAAAATCGAGGTTAGAGTATCCCCGATTAT
1 -GAAAAATTGTGTTTT-AGAAATAAAAT-GGGGTTAGAGTATCCCCGATTAT
*
631630 GAAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
1 GAAAAATTG-TGTTTTAGAAATAAAA-TGGGGTTAGAGTATCCCC
631675 TCGGAAATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
51 41 0.51
52 39 0.49
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.28
Consensus pattern (49 bp):
GAAAAATTGTGTTTTAGAAATAAAATGGGGTTAGAGTATCCCCGATTAT
Found at i:631748 original size:79 final size:79
Alignment explanation
Indices: 631609--631863 Score: 420
Period size: 79 Copynumber: 3.2 Consensus size: 79
631599 ATAAAATCGA
* *
631609 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
631674 CTCGGAAATAATGG
66 CTCGGAAATAACGG
* * *
631688 GATTGGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
631753 CTCAGAAATAACGG
66 CTCGGAAATAACGG
* * *
631767 GGTTGGAGTATCCCCGATTATGAAAATTTGATGTTTTAGAAATAAAGCTGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
631832 CTCGGAAATAACGG
66 CTCGGAAATAACGG
631846 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
631864 GATTAACGGG
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 162 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGGAAATAACGG
Found at i:631850 original size:28 final size:27
Alignment explanation
Indices: 631816--631889 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
631806 AAATAAAGCT
**
631816 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGAGG-AATAAC
* *
631844 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGAGGAATAAC
*
631871 GGGGTTAGAGTATCCCCGA
1 GGGGTTGGAGTATCCCCGA
631890 TTGTGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGAGGAATAAC
Found at i:633130 original size:28 final size:28
Alignment explanation
Indices: 633090--633170 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 28
633080 CTCATTTTCG
*
633090 TCCATGCTTTCATTTTTATGCCCATCAT
1 TCCATGCCTTCATTTTTATGCCCATCAT
633118 TCCATGCCTTCATTTTTTATTCCATGCCCATCAT
1 TCCATGCCTTCA---TTT-TT--ATGCCCATCAT
633152 TCCATGCCTTCATTTTTAT
1 TCCATGCCTTCATTTTTAT
633171 ATTCCATGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
28 13 0.28
30 2 0.04
31 6 0.13
32 2 0.04
34 23 0.50
ACGTcount: A:0.17, C:0.30, G:0.06, T:0.47
Consensus pattern (28 bp):
TCCATGCCTTCATTTTTATGCCCATCAT
Found at i:633145 original size:34 final size:35
Alignment explanation
Indices: 633107--633180 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
633097 TTTCATTTTT
633107 ATGCCCATCATTCCATGCCTTCATTTTT-TATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
633141 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
633176 ATGCC
1 ATGCC
633181 TTCATTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
34 28 0.72
35 11 0.28
ACGTcount: A:0.19, C:0.32, G:0.07, T:0.42
Consensus pattern (35 bp):
ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
Found at i:633208 original size:22 final size:21
Alignment explanation
Indices: 633150--633201 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
633140 CATGCCCATC
633150 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
633171 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
633192 ATTCCATGCC
1 ATTCCATGCC
633202 CATCATTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.27, G:0.06, T:0.48
Consensus pattern (21 bp):
ATTCCATGCCTTCATTTTTAT
Found at i:633209 original size:56 final size:55
Alignment explanation
Indices: 633116--633224 Score: 209
Period size: 56 Copynumber: 2.0 Consensus size: 55
633106 TATGCCCATC
633116 ATTCCATGCCTTCATTTTTTATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTTATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
633171 ATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGCCTTCATTTTT
1 ATTCCATGCCTTCATTTTT-TATTCCATGCCCATCATTCCATGCCTTCATTTTT
633225 TTTTATTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 19 0.36
56 34 0.64
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (55 bp):
ATTCCATGCCTTCATTTTTTATTCCATGCCCATCATTCCATGCCTTCATTTTTAT
Found at i:633257 original size:12 final size:13
Alignment explanation
Indices: 633237--633265 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
633227 TTATTATTTT
633237 TTTTGAATTTTAA
1 TTTTGAATTTTAA
633250 TTTT-AATTTTAA
1 TTTTGAATTTTAA
633262 TTTT
1 TTTT
633266 TGATTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:633390 original size:20 final size:19
Alignment explanation
Indices: 633344--633397 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
633334 TTAGGTGTCT
*
633344 ACAGTATCGATACACATTT
1 ACAGTATCGATACACATTC
* *
633363 AAATGTATCGATACAGATTGC
1 ACA-GTATCGATACACATT-C
633384 ACAGTATCGATACA
1 ACAGTATCGATACA
633398 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (19 bp):
ACAGTATCGATACACATTC
Found at i:633405 original size:13 final size:13
Alignment explanation
Indices: 633387--633411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
633377 AGATTGCACA
633387 GTATCGATACATT
1 GTATCGATACATT
633400 GTATCGATACAT
1 GTATCGATACAT
633412 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:633424 original size:20 final size:20
Alignment explanation
Indices: 633399--633450 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
633389 ATCGATACAT
**
633399 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
* *
633419 TGTATCGACACTTGAAAAAA
1 TGTATCGATACATGAAAAAA
633439 TGTATCGATACA
1 TGTATCGATACA
633451 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:633510 original size:13 final size:13
Alignment explanation
Indices: 633492--633517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
633482 ACACACAATA
633492 TGTATCGATACAT
1 TGTATCGATACAT
633505 TGTATCGATACAT
1 TGTATCGATACAT
633518 CCTAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:633533 original size:33 final size:32
Alignment explanation
Indices: 633472--633539 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
633462 GTAGCCAAAT
*
633472 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
633504 TTGTATCGATACATC-CTAAAATGTATCGATACA
1 TTGTATCGATACA-CAC-AAAATGTATCGATACA
633537 TTG
1 TTG
633540 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:637297 original size:17 final size:17
Alignment explanation
Indices: 637276--637310 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
637266 TTTCTTCAAC
*
637276 TTTTTTATTTACATATAA
1 TTTTTT-TTAACATATAA
637294 TTTTTTTTAACATATAA
1 TTTTTTTTAACATATAA
637311 ATGTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAACATATAA
Found at i:639370 original size:15 final size:17
Alignment explanation
Indices: 639338--639373 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
639328 GATATTGTTG
639338 AATTAAACTTGAGATTT
1 AATTAAACTTGAGATTT
639355 AATTAAA-TTG-GATTT
1 AATTAAACTTGAGATTT
639370 AATT
1 AATT
639374 GAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (17 bp):
AATTAAACTTGAGATTT
Found at i:640349 original size:20 final size:19
Alignment explanation
Indices: 640299--640355 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
640289 GTATCAATCT
**
640299 AATGTATCGATACATGTTC
1 AATGTATCGATACATGAAC
* *
640318 ATTGTATTGATACATGAAC
1 AATGTATCGATACATGAAC
640337 AAATGTATCGATACATGAA
1 -AATGTATCGATACATGAA
640356 ACTGGCAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATGAAC
Found at i:642036 original size:33 final size:33
Alignment explanation
Indices: 641999--642063 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
641989 TTTGAAGCAA
* * *
641999 TGTATTGATACAATTTATCATGTATCGATACAT
1 TGTATCGATACAATGTACCATGTATCGATACAT
*
642032 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
642064 AATAGTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:642037 original size:13 final size:13
Alignment explanation
Indices: 642019--642043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
642009 CAATTTATCA
642019 TGTATCGATACAT
1 TGTATCGATACAT
642032 TGTATCGATACA
1 TGTATCGATACA
642044 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:642137 original size:19 final size:19
Alignment explanation
Indices: 642093--642148 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
642083 CTGGCAGTTT
**
642093 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
642113 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
642132 CATGTATCGATACAATG
1 CATGTATCGATACAATG
642149 TTTCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:650760 original size:21 final size:21
Alignment explanation
Indices: 650735--650776 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
650725 TTACAAATGA
*
650735 GGTTATAATTAAATTTTAAAT
1 GGTTATAATTAAATTATAAAT
*
650756 GGTTATATTTAAATTATAAAT
1 GGTTATAATTAAATTATAAAT
650777 ATTTTTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (21 bp):
GGTTATAATTAAATTATAAAT
Found at i:653140 original size:17 final size:16
Alignment explanation
Indices: 653113--653160 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
653103 AGATAATTTT
653113 TATATTATTTATTTAAG
1 TATA-TATTTATTTAAG
*
653130 ATATATATTTAATTTGAG
1 -TATATATTT-ATTTAAG
*
653148 TAAATATTTATTT
1 TATATATTTATTT
653161 GAGACAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 13 0.48
18 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TATATATTTATTTAAG
Found at i:654638 original size:21 final size:21
Alignment explanation
Indices: 654598--654640 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
654588 GTCATTACTT
* *
654598 GGGTGTGGACACTAATAGCTA
1 GGGTGTGAACACTAACAGCTA
*
654619 GGGTGTGAACACTAGCAGCTA
1 GGGTGTGAACACTAACAGCTA
654640 G
1 G
654641 AGACCTACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGTGTGAACACTAACAGCTA
Found at i:658542 original size:40 final size:40
Alignment explanation
Indices: 658498--658590 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
658488 TGTAGCTTAG
* * ** * *
658498 TGTATTGATATATTTTGATATGTATTGATACGTTATGTCT
1 TGTATTGATATAATTTGAAATGTATCCATACATTATGTCC
*
658538 TGTATTGACATAATTTGAAATGTATCCATACATTATGTCC
1 TGTATTGATATAATTTGAAATGTATCCATACATTATGTCC
658578 TGTATTGATATAA
1 TGTATTGATATAA
658591 ATCAATACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (40 bp):
TGTATTGATATAATTTGAAATGTATCCATACATTATGTCC
Found at i:663256 original size:155 final size:154
Alignment explanation
Indices: 662973--663523 Score: 571
Period size: 155 Copynumber: 3.5 Consensus size: 154
662963 TAAGTTCAAG
* * * * * ** *
662973 AAAAATTATGAAAATGCCCCTAAGG-GATAACTTCGATGT-AGAAGTA-CCCAATACCCCTAAAA
1 AAAAATTACGAAAATGCCTCT-AGGAGATACCTTCAACGTGA-AAGTATCCCGGTACCCCTAAAG
*
663035 GACTTAAAAAGGACTATAAAAGGAATGAACCTA-TCGTAAATACCCACCTTTTGCATAAAAGCAG
64 GACTTAAAAAGGACTATAAAAGGGATGAACCTATTC-TAAATACCCA-CTTTTGCATAAAAGCAG
*
663099 ACCCGGTTATAACCTAAGACTTAGTTTT
127 ACCCGGTTATAACCTAGGACTTAGTTTT
* * **
663127 AGAAAATTACGAAAACGCCTCTAGGAGATACCTTCGACGTGAAAGTATCTTGGTACCCCTAAAGG
1 A-AAAATTACGAAAATGCCTCTAGGAGATACCTTCAACGTGAAAGTATCCCGGTACCCCTAAAGG
* **
663192 ACTT-AAAAGGACTATATAAGGGATGAACCTATTCTAAATACCCACTTTTGACATAAAAATAGAC
65 ACTTAAAAAGGACTATAAAAGGGATGAACCTATTCTAAATACCCACTTTTG-CATAAAAGCAGAC
* * *
663256 CTGATT-TGAACCTAGGAC-TCGATTTT
129 CCGGTTAT-AACCTAGGACTTAG-TTTT
* * **
663282 AAAAGATTACAAAAATGCCCCTAAGG-GATACCTTCAACGTGAAAGTATCCCAATACCCCTAAAG
1 AAAA-ATTACGAAAATGCCTCT-AGGAGATACCTTCAACGTGAAAGTATCCCGGTACCCCTAAAG
* * * * ** * *
663346 GACTTAAAAAAGACTATAAAAAGAGATGAACCTATCCTAAATACCTACCTTCGGCTTAAAAGCGG
64 GACTTAAAAAGGACTAT-AAAAGGGATGAACCTATTCTAAATACCCA-CTTTTGCATAAAAGCAG
* *
663411 ACTCGGTTATAACCTAGGACTCAGTTTT
127 ACCCGGTTATAACCTAGGACTTAGTTTT
*
663439 GAAAAAATTATGAAAATG-CTCCTAGGAGATTTACCTTCAACGTGAAAGTATCCCGGTACCCCTA
1 --AAAAATTACGAAAATGCCT-CTAGGAGA--TACCTTCAACGTGAAAGTATCCCGGTACCCCTA
663503 AAGGACTTAAAAAGGACTATA
61 AAGGACTTAAAAAGGACTATA
663524 CCCACCTTCG
Statistics
Matches: 328, Mismatches: 48, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
154 16 0.05
155 150 0.46
156 32 0.10
157 55 0.17
158 20 0.06
159 5 0.02
160 50 0.15
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (154 bp):
AAAAATTACGAAAATGCCTCTAGGAGATACCTTCAACGTGAAAGTATCCCGGTACCCCTAAAGGA
CTTAAAAAGGACTATAAAAGGGATGAACCTATTCTAAATACCCACTTTTGCATAAAAGCAGACCC
GGTTATAACCTAGGACTTAGTTTT
Found at i:669524 original size:36 final size:33
Alignment explanation
Indices: 669462--669548 Score: 86
Period size: 36 Copynumber: 2.6 Consensus size: 33
669452 CTAAGTGATT
* ***
669462 GAGAAGTTCTATCTTAGCCTTTGAAAAAAATAGGGA
1 GAGAGGTTCTATCTTAGCCCGCG-AAAAAATA--GA
*
669498 GAGAGGTTCTATCTTAGCCCGCGAAAAGATAGA
1 GAGAGGTTCTATCTTAGCCCGCGAAAAAATAGA
*
669531 GAG-GTTTCTATCTTAGCC
1 GAGAGGTTCTATCTTAGCC
669549 TTGAAAGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 14 0.31
33 5 0.11
35 7 0.16
36 19 0.42
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (33 bp):
GAGAGGTTCTATCTTAGCCCGCGAAAAAATAGA
Found at i:678753 original size:155 final size:153
Alignment explanation
Indices: 678269--679339 Score: 1151
Period size: 155 Copynumber: 6.9 Consensus size: 153
678259 CTAAATAGGA
* ** * *
678269 TGAACTTATCCTAAATACCCACCTTTAACATAAAAGTGAAC-CAGGTGACAACCTAGGACTCGGT
1 TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTC-GGTGACAACCTAGGACTCGGT
** * * * * * *
678333 TCTAAAAAATTACCAAAATGCTCTTATAGGTATACCTTCGACATGAAAGTATCCTGGTAACCCTA
65 TCTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTA-CCTGGCAA-CCTA
* * * *
678398 AAGGACTTCAAAGGACTATAAAAATGG
128 AAGGACTTAAAAAGACTA-GAAAAGGG
* * * * ** * **
678425 TGAACCTCTCCTAAATACCCACCTTTAGCATTAAAGTGGACTCGGTGTTAACCTAAGACTCAATT
1 TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTT
* * * * * ** * *
678490 -TTAAAAATTACAAAAATGCCCTTA-GGGGATACCTTCGACGTGAAAGTATATCGGTACCCTAAA
66 CTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTACCT-GGCAACCTAAA
* *
678553 GGACATAAAAAGACTAGAAATGGTG
130 GGACTTAAAAAGACTAGAAAAGG-G
* * * * * ** *
678578 ATGAACCTATCCCAAATGCCCACCTTCGGCATAAAAGCAGACCCGGTGGTAACCTAAGACTCGGT
1 -TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGT
* * * **
678643 TCTAAAAAATTACAAAAATACCCCTATGGGTATACGTTCGATATAAAAGTACCTGGGCAACCTAA
65 TCTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTACCT-GGCAACCTAA
*
678708 AGGACCTAAAAAGACTAGAAAAGGG
129 AGGACTTAAAAAGACTAGAAAAGGG
* *
678733 ATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGAT
1 -TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGT
* * * *
678798 TCTAAAAAATTATGAAAATGCCCCTATGGGTATACTTTCGACGTAAAAGCACCTAGTCAACCTAA
65 TCTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTACCT-GGCAACCT-A
*
678863 AAGGACTTAACAAGACTAGAAAAGGG
128 AAGGACTTAAAAAGACTAGAAAAGGG
* *
678889 TGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGATT
1 TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTT
* * * *
678954 CTAAAAAATTATGAAAATGCCCCTATGGGTATACTTTCGACGTAAAAGCACCTAGTCAACCTAAA
66 CTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTACCT-GGCAACCT-AA
*
679019 AGGACTTAACAAGACTAGAAAAGGG
129 AGGACTTAAAAAGACTAGAAAAGGG
* * * * *
679044 TGAACCTATCCTAAATACCCACCTTCGGCATAGAAGCAGACCCGGTGACAACCTAGGACTCAGTT
1 TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTT
** * * * *
679109 CTAGGAAATTATGAAAATGCCCCTATAGGTATACCTTCAACGTAAAAGTACCCTGACAACCTTAA
66 CTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTA-CCTGGCAACC-TAA
679174 AGGACTTAAAAAGACTAGAAAAGGG
129 AGGACTTAAAAAGACTAGAAAAGGG
* * * * *
679199 TGCACCTATCCTAAATACCCACCTTTGGCATAAAAACGGACTCGGTAATAACCTAAGACTCGGTT
1 TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTT
* ** * * * * * *
679264 CTAAAAAATTATAAAAATACCCCTAAAGG-ATACCTTCAACGTGAAAGTATCTTGGTACCCCTAC
66 CTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTA-CCTGGCA-ACCTAA
679328 AGGACTTAAAAA
129 AGGACTTAAAAA
679340 AGATAGGCAT
Statistics
Matches: 797, Mismatches: 108, Indels: 22
0.86 0.12 0.02
Matches are distributed among these distances:
152 4 0.01
153 21 0.03
154 115 0.14
155 524 0.66
156 132 0.17
157 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (153 bp):
TGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTT
CTAAAAAATTATAAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTACCTGGCAACCTAAAG
GACTTAAAAAGACTAGAAAAGGG
Found at i:680446 original size:22 final size:22
Alignment explanation
Indices: 680418--680459 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
680408 TCTCTTTGCT
*
680418 TTTGCTTGTTGTTTCTTCTTTC
1 TTTGCTTGCTGTTTCTTCTTTC
680440 TTTGCTTGCTGTTTCTTCTT
1 TTTGCTTGCTGTTTCTTCTT
680460 GCTGTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTGCTTGCTGTTTCTTCTTTC
Found at i:680456 original size:15 final size:14
Alignment explanation
Indices: 680436--680477 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
680426 TTGTTTCTTC
680436 TTTCTTTGCTTGCTG
1 TTTCTTT-CTTGCTG
680451 TTTC-TTCTTGCTG
1 TTTCTTTCTTGCTG
680464 TTTCTTTTCTTGCT
1 TTTC-TTTCTTGCT
680478 TATTGTTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.44
14 2 0.08
15 12 0.48
ACGTcount: A:0.00, C:0.21, G:0.14, T:0.64
Consensus pattern (14 bp):
TTTCTTTCTTGCTG
Found at i:680462 original size:13 final size:13
Alignment explanation
Indices: 680444--680469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
680434 TCTTTCTTTG
680444 CTTGCTGTTTCTT
1 CTTGCTGTTTCTT
680457 CTTGCTGTTTCTT
1 CTTGCTGTTTCTT
680470 TTCTTGCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.15, T:0.62
Consensus pattern (13 bp):
CTTGCTGTTTCTT
Found at i:680469 original size:32 final size:33
Alignment explanation
Indices: 680422--680497 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 33
680412 TTTGCTTTTG
* *
680422 CTTGTTGTTTCTTCTTTCTTTGCTTGCTGTTTC-TT
1 CTTGCTGTTTC-T-TTTC-TTGCTTACTGTTTCGTT
*
680457 CTTGCTGTTTCTTTTCTTGCTTATTGTTTCGTTT
1 CTTGCTGTTTCTTTTCTTGCTTACTGTTTCG-TT
680491 CTTGCTG
1 CTTGCTG
680498 CTGCTGTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 12 0.33
33 4 0.11
34 10 0.28
35 10 0.28
ACGTcount: A:0.01, C:0.20, G:0.16, T:0.63
Consensus pattern (33 bp):
CTTGCTGTTTCTTTTCTTGCTTACTGTTTCGTT
Found at i:681436 original size:14 final size:14
Alignment explanation
Indices: 681390--681451 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
681380 TAATTTGTAT
*
681390 AATTATATTATAAA
1 AATTAAATTATAAA
*
681404 AATT-AA-TAAAAA
1 AATTAAATTATAAA
681416 TAATTAAATTATAAA
1 -AATTAAATTATAAA
681431 AATTAAAATT-TAAA
1 AATT-AAATTATAAA
681445 AATTAAA
1 AATTAAA
681452 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.12
13 8 0.20
14 18 0.44
15 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTAAATTATAAA
Found at i:685890 original size:16 final size:16
Alignment explanation
Indices: 685845--685892 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
685835 TAATATTTTT
* *
685845 ATTTAAATCAGTTTAA
1 ATTTAAATTATTTTAA
*
685861 ATTTAGATTATTTTAA
1 ATTTAAATTATTTTAA
*
685877 ATTTAAATTTTTTTAA
1 ATTTAAATTATTTTAA
685893 GTTCTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:686178 original size:25 final size:26
Alignment explanation
Indices: 686149--686199 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
686139 TTAAATTTTG
* *
686149 TTTATTTATT-TTTTATTTTTCATAT
1 TTTATTTATTAATTTATTTTTAATAT
686174 TTTATTTATTAATTTATTTTTAATAT
1 TTTATTTATTAATTTATTTTTAATAT
686200 AAATATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTATTTATTAATTTATTTTTAATAT
Found at i:686302 original size:17 final size:17
Alignment explanation
Indices: 686280--686329 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
686270 ATTTTGTATC
686280 TATATTTTAATATTTAA
1 TATATTTTAATATTTAA
686297 TATATTTTAAT-TTTAA
1 TATATTTTAATATTTAA
686313 TA-ATTTTTAATTATTTA
1 TATA-TTTTAA-TATTTA
686330 TTTTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.03
16 13 0.43
17 12 0.40
18 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTAATATTTAA
Found at i:689518 original size:165 final size:164
Alignment explanation
Indices: 689329--689869 Score: 662
Period size: 165 Copynumber: 3.3 Consensus size: 164
689319 TCATTCAATG
* * * * *
689329 CATACTAAATCAGTTTTCAAAAATTCATTCATTTTCATGTGTTTTGAATATTTTT-CTTAAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
* * *
689393 TCCTTGTTTTCGAAAAATGGAGTTTTCTACTCCGTAAATATTTTCGGATGGATTTTT-TTTGTTT
66 TCCTT-TTTTCGAAATACGGAGTTTTCTACTCCGTAAATGTTTTCGGA-GGATTTTTCTTTGTTT
*
689457 TTGATTTTTAAAATTCATCAAATATATTTATTTATTT
129 TT-ATTTTTAAAATTTATCAAATATATTTATTTATTT
* * *
689494 TATATTAAATTAGTTTTTAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
* * * * *
689559 TTCTTATTTCCTAAATACGGAATTTTCTACTCCGTAAATGTTTTCAGAGAGATTTTTCTTTGTTT
66 TCCTT-TTTTCGAAATACGGAGTTTTCTACTCCGTAAATGTTTTCGGAG-GATTTTTCTTTGTTT
689624 TTAGTTTTTAAAATTTATCAAATATATTTATTTATTT
129 TTA-TTTTTAAAATTTATCAAATATATTTATTTATTT
*
689661 CATAATAAATCAGTTTTCAAAAATTCATTTA-TTTCATGAGTTTTG-ATTTTTTTCCTTGAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
* * *** * * *
689724 GTCCTATTTTT-GAAATACGAAGTTTTTTACAATGT-AATGTTTTTGGGGGGATTTTTCTTAGTT
66 -TCCT-TTTTTCGAAATACGGAGTTTTCTACTCCGTAAATG-TTTTCGGAGGATTTTTCTTTGTT
* *
689787 TTTAATTTTTTAAATTTATCAAATATAGTTATTTATTT
128 TTT-ATTTTTAAAATTTATCAAATATATTTATTTATTT
* * * *
689825 CATATTAAATAATTTTTCAAAAATTCTTTTATTTTCATAAGTTTT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTT
689870 TTTATTTTTC
Statistics
Matches: 325, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
164 78 0.24
165 103 0.32
166 75 0.23
167 69 0.21
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (164 bp):
CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
TCCTTTTTTCGAAATACGGAGTTTTCTACTCCGTAAATGTTTTCGGAGGATTTTTCTTTGTTTTT
ATTTTTAAAATTTATCAAATATATTTATTTATTT
Found at i:689809 original size:164 final size:166
Alignment explanation
Indices: 689329--690045 Score: 674
Period size: 166 Copynumber: 4.3 Consensus size: 166
689319 TCATTCAATG
* * * * *
689329 CATACTAAATCAGTTTTCAAAAATTCATTCATTTTCATGTGTTTTGAATATTTTT-CTTAAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
* * * * *
689393 TCCT-TGTTTTCGAAAAATGGAGTTTTCTACTCCGTAAATATTTTCGGATGGATTTTT-TTTGTT
66 TCCTAT-TTTT-GAAATACGAAGTTTTCTACTCCGTAAATGTTTTCGGAGGGATTTTTCTTTGTT
* *
689456 TTTGATTTTTAAAATTCATCAAATATATTTATTTATTT
129 TTTAATTTTTAAAATTTATCAAATATATTTATTTATTT
* * *
689494 TATATTAAATTAGTTTTTAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAA-T
* * * *
689559 TTCTTATTTCCT-AAATACGGAA-TTTTCTACTCCGTAAATGTTTTCAGAGAGATTTTTCTTTGT
65 TTCCTATTT-TTGAAATAC-GAAGTTTTCTACTCCGTAAATGTTTTCGGAGGGATTTTTCTTTGT
*
689622 TTTTAGTTTTTAAAATTTATCAAATATATTTATTTATTT
128 TTTTAATTTTTAAAATTTATCAAATATATTTATTTATTT
*
689661 CATAATAAATCAGTTTTCAAAAATTCATTTA-TTTCATGAGTTTTG-ATTTTTTTCCTTGAAATT
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
* *** * * *
689724 GTCCTATTTTTGAAATACGAAGTTTTTTACAATGT-AATGTTTTTGGGGGGATTTTTCTTAGTTT
66 -TCCTATTTTTGAAATACGAAGTTTTCTACTCCGTAAATGTTTTCGGAGGGATTTTTCTTTGTTT
* *
689788 TTAATTTTTTAAATTTATCAAATATAGTTATTTATTT
130 TTAATTTTTAAAATTTATCAAATATATTTATTTATTT
* * * * * *
689825 CATATTAAATAATTTTTCAAAAATTCTTTTATTTTCATAAGTTTT--TTTATTTTTCTTTGAAA-
1 CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATT-TTTTTCCTTGAAAT
* * * * ** *
689887 TTCTCT-TTTCCGTGAAAAACCAAG-TTTCTTGCTCCGTAAACATTTTC-GAGGGAATTTTTCTC
65 TTC-CTATTT--TTGAAATACGAAGTTTTC-TACTCCGTAAATGTTTTCGGAGGG-ATTTTTCTT
*** ** * * * *
689949 AACTTAAAATTTTTAAAATTCATCTAATAT-TGTCATTTAATT
125 TGTTTTTAATTTTTAAAATTTATCAAATATAT-TTATTTATTT
* * * * * *
689991 CAAATTAAATCAATTTTGAAAATTTCAAATTA-TTTCATGAATTTTGAATTTTTTT
1 CATATTAAATCAGTTTTCAAAAATTC-ATTTATTTTCATGAGTTTTGAATTTTTTT
690046 GCATATCTTG
Statistics
Matches: 453, Mismatches: 78, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
163 5 0.01
164 99 0.22
165 128 0.28
166 132 0.29
167 85 0.19
168 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (166 bp):
CATATTAAATCAGTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTTTCCTTGAAATT
TCCTATTTTTGAAATACGAAGTTTTCTACTCCGTAAATGTTTTCGGAGGGATTTTTCTTTGTTTT
TAATTTTTAAAATTTATCAAATATATTTATTTATTT
Found at i:689858 original size:19 final size:19
Alignment explanation
Indices: 689836--689879 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
689826 ATATTAAATA
689836 ATTTTTCAAAAATTCTTTT
1 ATTTTTCAAAAATTCTTTT
* * *
689855 A-TTTTCATAAGTTTTTTT
1 ATTTTTCAAAAATTCTTTT
689873 ATTTTTC
1 ATTTTTC
689880 TTTGAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTCAAAAATTCTTTT
Found at i:690026 original size:331 final size:330
Alignment explanation
Indices: 689290--690045 Score: 748
Period size: 331 Copynumber: 2.3 Consensus size: 330
689280 TTTCATGGGT
* * * * * * *
689290 TTAAGATTTTGAAAATTCATCAAATGT-TATCATTCAATGCATACTAAATCAGTTTTCAAAAATT
1 TTAAAATTTTTAAAATTCATCAAATATAT-TCATTTAATTCATAATAAATCAATTTTCAAAAATT
** * * * * *
689354 C-ATTCATTTTCATGTGTTTTGAATATTTTT-CTTAAAATT-TCCT-TGTTTTCGAAAAATGGAG
65 CAATT-A-TTTCATGAATTTTGAATTTTTTTCCTTGAAATTGTCCTAT-TTTT-GAAATACGAAG
* *** * * ** * *
689415 TTTTCTACTCCGTAAATATTTTCGGATGGATTTTTTTTGTTTTTGATTTTTAAAATTCATCAAAT
126 TTTTTTACAATGT-AATGTTTTTGGGGGGATTTTTTTAGTTTTTAATTTTTAAAATTCATCAAAT
* * * *
689480 ATATTTATTTATTTTATATTAAATTAGTTTTTAAAAATTCATTTATTTTCATGAGTTTTGAATTT
190 ATAGTTATTTATTTCATATTAAATTAATTTTTAAAAATTCATTTATTTTCATAAGTTTT-AATTT
* * * * **
689545 TTTTCCTTGAAATTTTCTTATTTCCTAAATACGGAATTTTCTACTCCGTAAATGTTTTCAGAGAG
254 TTTTCCTTGAAATTCTCTTATTTCCTAAAAACGCAAGTTTCTACTCCGTAAACATTTTCAGAGAG
****
689610 ATTTTTCTTTGT
319 ATTTTTCTCAAC
** * * * * *
689622 TTTTAGTTTTTAAAATTTATCAAATATATTTATTTATTTCATAATAAATCAGTTTTCAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATATTCATTTAATTCATAATAAATCAATTTTCAAAAATTC
* *
689687 ATTTATTTCATGAGTTTTG-ATTTTTTTCCTTGAAATTGTCCTATTTTTGAAATACGAAGTTTTT
66 AATTATTTCATGAATTTTGAATTTTTTTCCTTGAAATTGTCCTATTTTTGAAATACGAAGTTTTT
* *
689751 TACAATGTAATGTTTTTGGGGGGATTTTTCTTAGTTTTTAATTTTTTAAATTTATCAAATATAGT
131 TACAATGTAATGTTTTTGGGGGGATTTTT-TTAGTTTTTAATTTTTAAAATTCATCAAATATAGT
* *
689816 TATTTATTTCATATTAAA-TAATTTTTCAAAAATTCTTTTATTTTCATAAGTTTT-TTTATTTTT
195 TATTTATTTCATATTAAATTAATTTTT-AAAAATTCATTTATTTTCATAAGTTTTAATT-TTTTT
* * *
689879 CTTTGAAATTCTC-T-TTTCCGTGAAAAAC-CAAGTTTCTTGCTCCGTAAACATTTTC-GAGGGA
258 CCTTGAAATTCTCTTATTTCC-T-AAAAACGCAAGTTTC-TACTCCGTAAACATTTTCAGAGAG-
689940 ATTTTTCTCAAC
319 ATTTTTCTCAAC
* * *
689952 TTAAAATTTTTAAAATTCATCTAATAT-TGTCATTTAATTCA-AATTAAATCAATTTTGAAAATT
1 TTAAAATTTTTAAAATTCATCAAATATAT-TCATTTAATTCATAA-TAAATCAATTTTCAAAAAT
690015 TCAAATTATTTCATGAATTTTGAATTTTTTT
64 TC-AATTATTTCATGAATTTTGAATTTTTTT
690046 GCATATCTTG
Statistics
Matches: 346, Mismatches: 62, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
328 5 0.01
329 17 0.05
330 125 0.36
331 127 0.37
332 68 0.20
333 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (330 bp):
TTAAAATTTTTAAAATTCATCAAATATATTCATTTAATTCATAATAAATCAATTTTCAAAAATTC
AATTATTTCATGAATTTTGAATTTTTTTCCTTGAAATTGTCCTATTTTTGAAATACGAAGTTTTT
TACAATGTAATGTTTTTGGGGGGATTTTTTTAGTTTTTAATTTTTAAAATTCATCAAATATAGTT
ATTTATTTCATATTAAATTAATTTTTAAAAATTCATTTATTTTCATAAGTTTTAATTTTTTTCCT
TGAAATTCTCTTATTTCCTAAAAACGCAAGTTTCTACTCCGTAAACATTTTCAGAGAGATTTTTC
TCAAC
Found at i:690512 original size:22 final size:21
Alignment explanation
Indices: 690481--690525 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
690471 AGATCAACTG
* *
690481 AAAAAGAAGAGCAAAAAAGAGA
1 AAAAAGAAGA-AAAAAAAAAGA
*
690503 AAAAATAAGAAAAAAAAAAGA
1 AAAAAGAAGAAAAAAAAAAGA
690524 AA
1 AA
690526 TTAGTTAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAAGAAGAAAAAAAAAAGA
Found at i:692010 original size:156 final size:154
Alignment explanation
Indices: 691704--692244 Score: 538
Period size: 156 Copynumber: 3.5 Consensus size: 154
691694 TTCCCTCATG
* * * * * * * * *
691704 TTTTAAATCTTTTAGGGGTATCA-ACTACTTTTATGTCAAAGGTATCCTTTAGGAGCATTTTCAT
1 TTTTAAGTCCTTTAGGGGTATCAGGC-ACTTCTATGTCGAAGATATCCCTTAGG-GTATTTTGAT
* * * * * * * * *
691768 AA-TTTTTAAAACCAACTCCTAGGTCATTACGGGGTTCGCTTTTATGCCGAAGGTAGATATCTAA
64 AATTTTTTGAAACCAAGTCCTAAGTTATCACCGGGTTCGCTTTTATGCCGAAGGTGGGTATTTAA
**
691832 GATATTTTCATCCCATTTTATAATCTC
129 GATAGGTTCATCCCA-TTTATAATCTC
*
691859 TTTTAAGTCCTTTAGGGGTATCAGGCACTTCTATGTC-ATAGATATCCTCTAAGGGTATTTTGAT
1 TTTTAAGTCCTTTAGGGGTATCAGGCACTTCTATGTCGA-AGATATCC-CTTAGGGTATTTTGAT
* * * * *
691923 AATTTTTT-AGAATCGAGTCCTAAGTTGTCACTGGGTTCGCTTTTATGCCGAAGGTGGGTATTTG
64 AATTTTTTGA-AACCAAGTCCTAAGTTATCACCGGGTTCGCTTTTATGCCGAAGGTGGGTATTTA
* *
691987 TGATAGGTTCATCCCATTCTATAATCCC
128 AGATAGGTTCATCCCATT-TATAATCTC
* ** * *
692015 TTTTAAGTCCTTTAAGAATATCAGGCACTTCTACGTCGAAGATATCCCTTAGGGACATTTTGATA
1 TTTTAAGTCCTTTAGGGGTATCAGGCACTTCTATGTCGAAGATATCCCTTAGGG-TATTTTGATA
* * * * *
692080 ATTTTTTGAAACCAAGTTCTACGTTATCACCGGG-TCTGTTTTTATACCAAAGGTGGGTATTTAA
65 ATTTTTTGAAACCAAGTCCTAAGTTATCACCGGGTTC-GCTTTTATGCCGAAGGTGGGTATTTAA
*
692144 GATAGGTTCATCCCATTTAGAATGCT-
129 GATAGGTTCATCCCATTTATAAT-CTC
* * * *
692170 TTTTAAGTCCTTTAGAGGTATCGGGTACTTCTATGTCGAAGGTATCCCTTAGAGGTATTTTCG-T
1 TTTTAAGTCCTTTAGGGGTATCAGGCACTTCTATGTCGAAGATATCCCTTAG-GGTATTTT-GAT
692234 AATTTTTTGAA
64 AATTTTTTGAA
692245 CTTAACCCTT
Statistics
Matches: 320, Mismatches: 53, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
154 1 0.00
155 125 0.39
156 192 0.60
157 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (154 bp):
TTTTAAGTCCTTTAGGGGTATCAGGCACTTCTATGTCGAAGATATCCCTTAGGGTATTTTGATAA
TTTTTTGAAACCAAGTCCTAAGTTATCACCGGGTTCGCTTTTATGCCGAAGGTGGGTATTTAAGA
TAGGTTCATCCCATTTATAATCTC
Found at i:696962 original size:77 final size:80
Alignment explanation
Indices: 696810--696972 Score: 188
Period size: 77 Copynumber: 2.1 Consensus size: 80
696800 GAATTTGTTG
* * * * * **
696810 TTTTACTGATAGTTGCATTTACATCGTTTCATGCACATTTGCATGAAATTAGTATTTGCATTGTT
1 TTTTACTAATACTTGCATCTACATCGTTTCA-GCACATTTACATGAAATTAGCATTTGCATCATT
* *
696875 TCATATGCATTTACCA
65 CCATAAGCATTTACCA
* *
696891 TTTTACTAATACTTGCATCTACATCGTTT-A-CA-TTTTACATGACATTAGCATTTGCATCATTC
1 TTTTACTAATACTTGCATCTACATCGTTTCAGCACATTTACATGAAATTAGCATTTGCATCATTC
*
696953 CATAAGCATTTGCCA
66 CATAAGCATTTACCA
696968 TTTTA
1 TTTTA
696973 TTGAAACTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 41 0.59
78 2 0.03
80 1 0.01
81 26 0.37
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (80 bp):
TTTTACTAATACTTGCATCTACATCGTTTCAGCACATTTACATGAAATTAGCATTTGCATCATTC
CATAAGCATTTACCA
Found at i:702242 original size:51 final size:51
Alignment explanation
Indices: 702137--702284 Score: 233
Period size: 51 Copynumber: 2.9 Consensus size: 51
702127 CGAAATATGA
* *
702137 AAATTTGTCTGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTT-ATAGTGTATCGATACATCTGGGC
702189 AAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
***
702240 AAATTTGCCTGCATGTATCGATACAAAGATGAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTAT-AGTGTATCGATACA
702285 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 49 0.54
52 41 0.46
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
Found at i:702291 original size:13 final size:13
Alignment explanation
Indices: 702273--702297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
702263 CAAAGATGAG
702273 TGTATCGATACAA
1 TGTATCGATACAA
702286 TGTATCGATACA
1 TGTATCGATACA
702298 TTTGGATAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:702367 original size:19 final size:19
Alignment explanation
Indices: 702343--702455 Score: 124
Period size: 19 Copynumber: 6.5 Consensus size: 19
702333 CTTACATTGC
*
702343 ATCGATACAAAACTTATGT
1 ATCGATACAACACTTATGT
702362 ATCGAT---ACA--T-TGT
1 ATCGATACAACACTTATGT
702375 ATCGATACAACACTTATGT
1 ATCGATACAACACTTATGT
702394 ATCGAT---ACA--T-TGT
1 ATCGATACAACACTTATGT
702407 ATCGATACAACACTTATGT
1 ATCGATACAACACTTATGT
702426 ATCGATACAACACTTTATGT
1 ATCGATACAACAC-TTATGT
702446 ATCGATACAA
1 ATCGATACAA
702456 ATCGTTGAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 25
0.75 0.01 0.24
Matches are distributed among these distances:
13 18 0.22
14 2 0.03
16 11 0.14
18 2 0.03
19 31 0.39
20 16 0.20
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
ATCGATACAACACTTATGT
Found at i:702377 original size:13 final size:13
Alignment explanation
Indices: 702359--702415 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
702349 ACAAAACTTA
702359 TGTATCGATACAT
1 TGTATCGATACAT
702372 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
702390 ATGTATCGATACAT
1 -TGTATCGATACAT
702404 TGTATCGATACA
1 TGTATCGATACA
702416 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:702379 original size:32 final size:32
Alignment explanation
Indices: 702335--702434 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
702325 GGCAGTAGCT
* *
702335 TACATTGCATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
702367 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
702399 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
702431 TACA
1 TACA
702435 ACACTTTATG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:702533 original size:21 final size:21
Alignment explanation
Indices: 702492--702533 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
702482 GTTGGGACCT
*
702492 TGTATCGATACATTCTAACAA
1 TGTATCGATACATTCGAACAA
*
702513 TGTATCGATACATTCGGACAA
1 TGTATCGATACATTCGAACAA
702534 AAATGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATTCGAACAA
Done.