Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:4751660 original size:20 final size:21
Alignment explanation
Indices: 4751631--4751672 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4751621 ATTAATAACA
4751631 TTTAAAAGAAAATT-TTATAT
1 TTTAAAAGAAAATTATTATAT
*
4751651 TTTAATAGAAAATTATTATAT
1 TTTAAAAGAAAATTATTATAT
4751672 T
1 T
4751673 AAAGGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAAAAGAAAATTATTATAT
Found at i:4763885 original size:20 final size:20
Alignment explanation
Indices: 4763860--4763914 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
4763850 GGTGGATGTT
4763860 ATCTATCGATAGATGAGACC
1 ATCTATCGATAGATGAGACC
* **
4763880 ATCTATTGATAGATTTGACC
1 ATCTATCGATAGATGAGACC
* *
4763900 ATTTATCTATAGATG
1 ATCTATCGATAGATG
4763915 TTCTTAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (20 bp):
ATCTATCGATAGATGAGACC
Found at i:4767674 original size:16 final size:16
Alignment explanation
Indices: 4767649--4767680 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4767639 TTTGTTGGGC
4767649 CTCTTGTTTTTTTTTT
1 CTCTTGTTTTTTTTTT
4767665 CTCTT-TTTTTTTTTT
1 CTCTTGTTTTTTTTTT
4767680 C
1 C
4767681 GTTAGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
CTCTTGTTTTTTTTTT
Found at i:4768351 original size:22 final size:22
Alignment explanation
Indices: 4768325--4768382 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4768315 CTAACTTTGG
* * *
4768325 GCATTGCGTGATTACTTTTTAA
1 GCATTGCATGACTAATTTTTAA
*
4768347 GCATTCCATGACTAATTTTTAA
1 GCATTGCATGACTAATTTTTAA
*
4768369 GTATTGCATGACTA
1 GCATTGCATGACTA
4768383 GTTGGTAGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (22 bp):
GCATTGCATGACTAATTTTTAA
Found at i:4768464 original size:22 final size:22
Alignment explanation
Indices: 4768434--4768502 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
4768424 ACTTAGACAT
*
4768434 TGCTTAAAAATCAGTCACGCAA
1 TGCTCAAAAATCAGTCACGCAA
* *
4768456 TGCTCAAAAATTAGTCATGCAA
1 TGCTCAAAAATCAGTCACGCAA
* * *
4768478 TAC-CTAAAAACCAGTCACGTAA
1 TGCTC-AAAAATCAGTCACGCAA
4768500 TGC
1 TGC
4768503 CTATAACTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (22 bp):
TGCTCAAAAATCAGTCACGCAA
Found at i:4770403 original size:16 final size:18
Alignment explanation
Indices: 4770364--4770404 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4770354 ATTTTTTTCA
*
4770364 TTTATTATTATTTATTAT
1 TTTAATATTATTTATTAT
4770382 TGTTAATATT-TTTATT-T
1 T-TTAATATTATTTATTAT
4770399 TTTAAT
1 TTTAAT
4770405 TTTGATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 2 0.10
18 7 0.33
19 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTAATATTATTTATTAT
Found at i:4786945 original size:17 final size:17
Alignment explanation
Indices: 4786915--4786971 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
4786905 AGGCCGACGG
*
4786915 GGAGAAAAATGAAGAAGA
1 GGAGAAAAAAGAAGAA-A
4786933 GGA-AAAAAAGAAGAAA
1 GGAGAAAAAAGAAGAAA
*
4786949 -GAGAAAGAAGAAGAAAA
1 GGAGAAAAAAGAAG-AAA
4786966 GGAGAA
1 GGAGAA
4786972 GGAAAAGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
17 14 0.41
18 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (17 bp):
GGAGAAAAAAGAAGAAA
Found at i:4787077 original size:48 final size:45
Alignment explanation
Indices: 4787025--4787114 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 45
4787015 AGAGGAAGAA
4787025 GAAAGAAAAAGAAAGAAAAAAGAGAAGAGGAAAGACAGAGA-AAGAGGC
1 GAAAG-AAAA-AAAGAAAAAAGAGAAGA-GAAAGA-AGAGAGAAGAGGC
* **
4787073 GAAAGAAAAAAGGAAGGAAGAGAAGAGAAAGAAGAGAGAAGA
1 GAAAGAAAAAAAGAAAAAAGAGAAGAGAAAGAAGAGAGAAGA
4787115 ACGGCTAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 5 0.13
45 10 0.26
46 14 0.37
47 4 0.11
48 5 0.13
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (45 bp):
GAAAGAAAAAAAGAAAAAAGAGAAGAGAAAGAAGAGAGAAGAGGC
Found at i:4787108 original size:38 final size:38
Alignment explanation
Indices: 4787035--4787110 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 38
4787025 GAAAGAAAAA
* *
4787035 GAAAGAAAAAAGAGAAGAGGAAAGACAGAGAAAGAGGC
1 GAAAGAAAAAAGAGAAGAAGAAAGACAAAGAAAGAGGC
*
4787073 GAAAGAAAAAAG-GAAGGAAGAGAAGAGAAAGAAGAGAG
1 GAAAGAAAAAAGAGAA-GAAGA-AAGACAAAGAA-AGAG
4787111 AAGAACGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 16 0.50
39 9 0.28
40 4 0.12
ACGTcount: A:0.62, C:0.03, G:0.36, T:0.00
Consensus pattern (38 bp):
GAAAGAAAAAAGAGAAGAAGAAAGACAAAGAAAGAGGC
Found at i:4787115 original size:14 final size:14
Alignment explanation
Indices: 4787019--4787109 Score: 53
Period size: 14 Copynumber: 6.1 Consensus size: 14
4787009 AGAAGGAGAG
*
4787019 GAAGAAGAAAGAAAAA
1 GAAG-AGAAAG-AAGA
*
4787035 GAA-AGAAAAAAGA
1 GAAGAGAAAGAAGA
4787048 GAAGAGGAAAGACAGA
1 GAAGA-GAAAGA-AGA
4787064 GAAAGAGGCGAAAGAA-A
1 G-AAGA---GAAAGAAGA
* *
4787081 AAAG-GAAGGAAGA
1 GAAGAGAAAGAAGA
4787094 GAAGAGAAAGAAGA
1 GAAGAGAAAGAAGA
4787108 GA
1 GA
4787110 GAAGAACGGC
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
12 6 0.10
13 10 0.17
14 16 0.27
15 5 0.08
16 10 0.17
17 5 0.08
18 1 0.02
19 6 0.10
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAGAGAAAGAAGA
Found at i:4787155 original size:2 final size:2
Alignment explanation
Indices: 4787148--4787179 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4787138 AGAGAAAGTG
4787148 AT AT AT AT AT AT A- 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 A
4787180 AGAGAACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4787924 original size:19 final size:19
Alignment explanation
Indices: 4787849--4787932 Score: 62
Period size: 22 Copynumber: 4.1 Consensus size: 19
4787839 TTTGTTAATC
4787849 ATAGCAATATAAAATGAATAAA
1 ATAGCAATA-AAAA--AATAAA
*
4787871 ATA-CATATAAATAAATAATA
1 ATAGCA-ATAAAAAAATAA-A
* *
4787891 ATTATGAAATTAAAAAATAAA
1 A-TA-GCAATAAAAAAATAAA
4787912 ATAGCAATAAAAAAATTAAA
1 ATAGCAATAAAAAAA-TAAA
4787932 A
1 A
4787933 AAATTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
19 15 0.30
20 9 0.18
21 9 0.18
22 16 0.32
23 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (19 bp):
ATAGCAATAAAAAAATAAA
Found at i:4787945 original size:10 final size:9
Alignment explanation
Indices: 4787919--4787944 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4787909 AAAATAGCAA
4787919 TAAAAAAAT
1 TAAAAAAAT
4787928 TAAAAAAAT
1 TAAAAAAAT
4787937 TAAAAAAA
1 TAAAAAAA
4787945 AACTTTGGTA
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:0.00, T:0.19
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:4792197 original size:10 final size:10
Alignment explanation
Indices: 4792154--4792202 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
4792144 TTTCTTCTAG
4792154 TTTTCTTTCGTT
1 TTTTCTTT--TT
*
4792166 TTTTGCTTCTT
1 TTTT-CTTTTT
4792177 TTTTCTTTTT
1 TTTTCTTTTT
4792187 TTTTCTTTTT
1 TTTTCTTTTT
4792197 TTTTCT
1 TTTTCT
4792203 ATTTGTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 21 0.62
11 6 0.18
12 4 0.12
13 3 0.09
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:4798413 original size:15 final size:15
Alignment explanation
Indices: 4798395--4798425 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4798385 TAATTTTATT
4798395 TTTTTTAAAAAATTA
1 TTTTTTAAAAAATTA
*
4798410 TTTTTTAAGAAATTA
1 TTTTTTAAAAAATTA
4798425 T
1 T
4798426 CAAAATTTTT
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTTTAAAAAATTA
Found at i:4798872 original size:16 final size:17
Alignment explanation
Indices: 4798843--4798874 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4798833 AATTGGCTTC
4798843 TTCTTCTCCTTCGTTTG
1 TTCTTCTCCTTCGTTTG
4798860 TTCTTCT-CTTCGTTT
1 TTCTTCTCCTTCGTTT
4798875 TACAAGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.28, G:0.09, T:0.62
Consensus pattern (17 bp):
TTCTTCTCCTTCGTTTG
Found at i:4814522 original size:18 final size:18
Alignment explanation
Indices: 4814495--4814531 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4814485 ATACCTTGAA
*
4814495 AAAACGTTAACAGTGTAC
1 AAAACATTAACAGTGTAC
4814513 AAAACATTAACAGTGTAC
1 AAAACATTAACAGTGTAC
4814531 A
1 A
4814532 TTATATGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (18 bp):
AAAACATTAACAGTGTAC
Found at i:4825069 original size:51 final size:51
Alignment explanation
Indices: 4824993--4825094 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
4824983 NNNNNAATCG
* *
4824993 GAATAAGTAATTCGAATCCCATTAAAGATAAGTAAGAAAGAGATTAAAAAT
1 GAATAAGCAATTAGAATCCCATTAAAGATAAGTAAGAAAGAGATTAAAAAT
4825044 GAATAAGCAATTAGAATCCCATTAAAGATAAGTAAGAAAGAGATTAAAAAT
1 GAATAAGCAATTAGAATCCCATTAAAGATAAGTAAGAAAGAGATTAAAAAT
4825095 TATATAACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.23
Consensus pattern (51 bp):
GAATAAGCAATTAGAATCCCATTAAAGATAAGTAAGAAAGAGATTAAAAAT
Found at i:4828497 original size:12 final size:13
Alignment explanation
Indices: 4828468--4828504 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
4828458 AATTTTGGAT
*
4828468 AAAAATTTTAGTC
1 AAAAATTTCAGTC
4828481 AAAAATTTCAGTC
1 AAAAATTTCAGTC
4828494 AAAAATTTCAG
1 AAAAATTTCAG
4828505 CACGTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (13 bp):
AAAAATTTCAGTC
Found at i:4834264 original size:21 final size:22
Alignment explanation
Indices: 4834235--4834278 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4834225 AAGTGATTAA
4834235 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
4834256 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
4834278 T
1 T
4834279 ACTTTGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:4844094 original size:29 final size:28
Alignment explanation
Indices: 4844033--4844088 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
4844023 GGGAGCAAGG
*
4844033 ATAACCTTTTGCCTTTCAAGGATTAGGC
1 ATAACCTTTTGCCTTTCAAGGATTAAGC
4844061 ATAACCTCTTT-CCTTTTCAAGGATTAAG
1 ATAACCT-TTTGCC-TTTCAAGGATTAAG
4844089 TGTAACTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (28 bp):
ATAACCTTTTGCCTTTCAAGGATTAAGC
Found at i:4844672 original size:43 final size:42
Alignment explanation
Indices: 4844596--4844689 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
4844586 TTCATTCCTA
*
4844596 AGATATCAGTTTTTCTTGCTTGAAAATCGATTCTTGCCTCTCC
1 AGATATCAGTTTTTCTTGCTTGAAAATC-ATTCTTACCTCTCC
* *
4844639 AGATATTAGTTTTTCTTGTTTAAGAAAAT-ATTCTTACCTCTCC
1 AGATATCAGTTTTTCTTGCTT--GAAAATCATTCTTACCTCTCC
*
4844682 ATATATCA
1 AGATATCA
4844690 ATTAGTCCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 38 0.86
45 6 0.14
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.44
Consensus pattern (42 bp):
AGATATCAGTTTTTCTTGCTTGAAAATCATTCTTACCTCTCC
Found at i:4845057 original size:20 final size:20
Alignment explanation
Indices: 4845032--4845074 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4845022 CACCCCATTG
*
4845032 CTCTTGAATGTTTCACATAT
1 CTCTTGAATGTTCCACATAT
4845052 CTCTTGAATGTTCCACATAT
1 CTCTTGAATGTTCCACATAT
4845072 CTC
1 CTC
4845075 CAAGAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (20 bp):
CTCTTGAATGTTCCACATAT
Found at i:4847009 original size:10 final size:10
Alignment explanation
Indices: 4846980--4847023 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
4846970 TAACTTTTCT
*
4846980 TAAAGTAAAT
1 TAAAGTAAAA
4846990 TAAAGTAAAA
1 TAAAGTAAAA
4847000 TAAAGTAAAA
1 TAAAGTAAAA
4847010 TTACAA-TAAAA
1 -TA-AAGTAAAA
4847021 TAA
1 TAA
4847024 CTTAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 1 0.03
10 21 0.68
11 7 0.23
12 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (10 bp):
TAAAGTAAAA
Found at i:4847029 original size:21 final size:21
Alignment explanation
Indices: 4846980--4847023 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4846970 TAACTTTTCT
4846980 TAAAGT-AAATTAAAGTAAAA
1 TAAAGTAAAATTAAAGTAAAA
4847000 TAAAGTAAAATTACAA-TAAAA
1 TAAAGTAAAATTA-AAGTAAAA
4847021 TAA
1 TAA
4847024 CTTAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAAGTAAAATTAAAGTAAAA
Found at i:4849671 original size:28 final size:28
Alignment explanation
Indices: 4849632--4849694 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
4849622 CAATGCACAC
*
4849632 TGCC-TTTTATGGATCAAGCATAACTAT
1 TGCCTTTTTATGGATCAAGCATAACCAT
*
4849659 TGCCTTTTTATGGATCAAGCATAGCCAT
1 TGCCTTTTTATGGATCAAGCATAACCAT
4849687 TGCCTTTT
1 TGCCTTTT
4849695 CAAGATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (28 bp):
TGCCTTTTTATGGATCAAGCATAACCAT
Found at i:4851086 original size:31 final size:33
Alignment explanation
Indices: 4851017--4851086 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
4851007 AACCTTTACA
* *
4851017 CTTTTCACAAGATCAAGTACAACTTTTACAATAC
1 CTTTTCACAAGATCAAGCACAACTCTTAC-ATAC
4851051 CTTTTC-CAAGAATCAAGCACAAC-CTTAC-TAC
1 CTTTTCACAAG-ATCAAGCACAACTCTTACATAC
4851082 CTTTT
1 CTTTT
4851087 ACTTAGGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
33 8 0.24
34 17 0.52
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (33 bp):
CTTTTCACAAGATCAAGCACAACTCTTACATAC
Found at i:4855136 original size:12 final size:12
Alignment explanation
Indices: 4855120--4855162 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
4855110 AAAGAAAGCA
4855120 AAAAATATGAAAT
1 AAAAA-ATGAAAT
*
4855133 AAAAAATGAATT
1 AAAAAATGAAAT
4855145 AAAAAAT-AAAT
1 AAAAAATGAAAT
4855156 AATAAAA
1 AA-AAAA
4855163 GATTATACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAATGAAAT
Found at i:4856298 original size:23 final size:24
Alignment explanation
Indices: 4856246--4856299 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
4856236 AAATATGCTA
* *
4856246 TTATAAATATTTTTAATAACAATT
1 TTATAAATACTTTTAAGAACAATT
*
4856270 TT-TAAATACTTTT-AGAACATTT
1 TTATAAATACTTTTAAGAACAATT
4856292 TTATAAAT
1 TTATAAAT
4856300 TTGATTTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATAAATACTTTTAAGAACAATT
Found at i:4858232 original size:18 final size:17
Alignment explanation
Indices: 4858209--4858242 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4858199 TTTATCGGTA
4858209 TGATCTTATATATGATTC
1 TGATCTTATATA-GATTC
*
4858227 TGATCTTGTATAGATT
1 TGATCTTATATAGATT
4858243 AATACTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (17 bp):
TGATCTTATATAGATTC
Found at i:4873414 original size:22 final size:22
Alignment explanation
Indices: 4873389--4873432 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4873379 GCATTACAAA
* *
4873389 AATGGATATTAGGCATTGTGTG
1 AATGGATATTAAGCAATGTGTG
4873411 AATGGATATTAAGCAATGTGTG
1 AATGGATATTAAGCAATGTGTG
4873433 CTTGGTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (22 bp):
AATGGATATTAAGCAATGTGTG
Found at i:4873470 original size:21 final size:22
Alignment explanation
Indices: 4873434--4873477 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4873424 CAATGTGTGC
*
4873434 TTGGTTGTTATGTATTTCGTGA
1 TTGGTTGTTATGTATTGCGTGA
*
4873456 TTGGTT-TTTTGTATTGCGTGA
1 TTGGTTGTTATGTATTGCGTGA
4873477 T
1 T
4873478 GTAGAGCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.11, C:0.05, G:0.27, T:0.57
Consensus pattern (22 bp):
TTGGTTGTTATGTATTGCGTGA
Found at i:4877842 original size:22 final size:23
Alignment explanation
Indices: 4877816--4877859 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4877806 AACATGTTAA
4877816 CATA-TCATACAT-CAAAACACAT
1 CATATTCA-ACATGCAAAACACAT
*
4877838 CATATTCAACATGCATAACACA
1 CATATTCAACATGCAAAACACA
4877860 AAAAAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (23 bp):
CATATTCAACATGCAAAACACAT
Found at i:4885692 original size:23 final size:23
Alignment explanation
Indices: 4885669--4885753 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
4885659 TGACCCTATG
* *
4885669 AACCAATCACGCAATAACATATG
1 AACCAATCACGCAATGACATATC
* * *
4885692 AA-CAACTTACGCAATGACCTAAC
1 AACCAA-TCACGCAATGACATATC
* *
4885715 AACTAGTCACGCAATGACATATC
1 AACCAATCACGCAATGACATATC
* *
4885738 AACCAGTCACACAATG
1 AACCAATCACGCAATG
4885754 CCTAAACCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 3 0.06
23 44 0.92
24 1 0.02
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.18
Consensus pattern (23 bp):
AACCAATCACGCAATGACATATC
Found at i:4885787 original size:21 final size:20
Alignment explanation
Indices: 4885749--4885787 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4885739 ACCAGTCACA
*
4885749 CAATGCCTAAACCTTAATCG
1 CAATGCCTAAACCCTAATCG
4885769 CAATGCCTAAAACCCTAAT
1 CAATGCCT-AAACCCTAAT
4885788 TGACGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (20 bp):
CAATGCCTAAACCCTAATCG
Found at i:4890342 original size:2 final size:2
Alignment explanation
Indices: 4890335--4890382 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4890325 AAATACATAG
4890335 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
4890377 TA TA TA
1 TA TA TA
4890383 CATTTGCCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4897098 original size:22 final size:22
Alignment explanation
Indices: 4897067--4897126 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
4897057 GGAAAGTCGC
*
4897067 CCAGCGCTGCAGCGCTACTTTT
1 CCAGCACTGCAGCGCTACTTTT
*
4897089 CCAGCACTGCAGTGCTACTTTT
1 CCAGCACTGCAGCGCTACTTTT
4897111 CCAGCACTGCAGCGCT
1 CCAGCACTGCAGCGCT
4897127 GAGCTCTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.37, G:0.22, T:0.25
Consensus pattern (22 bp):
CCAGCACTGCAGCGCTACTTTT
Found at i:4902588 original size:25 final size:25
Alignment explanation
Indices: 4902560--4902618 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
4902550 GTAGTCGTAA
**
4902560 CCACATATATCAACTTGTGGCCTAG
1 CCACATATATCAACCCGTGGCCTAG
*
4902585 CCACATATATCAACCCGTGGCCTTG
1 CCACATATATCAACCCGTGGCCTAG
*
4902610 CCACGTATA
1 CCACATATA
4902619 CATCACAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCGTGGCCTAG
Found at i:4907766 original size:31 final size:31
Alignment explanation
Indices: 4907728--4907787 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
4907718 TTCTACCTTA
*
4907728 GGATCACCTTGGTTGTTTAATGCAAAGGTTT
1 GGATCACCTTAGTTGTTTAATGCAAAGGTTT
4907759 GGATCACCTTAGTTGTTTAATGCAAAGGT
1 GGATCACCTTAGTTGTTTAATGCAAAGGT
4907788 AAGCACCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (31 bp):
GGATCACCTTAGTTGTTTAATGCAAAGGTTT
Found at i:4914338 original size:2 final size:2
Alignment explanation
Indices: 4914331--4914356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4914321 AGTAAATTTC
4914331 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
4914357 ATTATGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4917130 original size:343 final size:338
Alignment explanation
Indices: 4916472--4917156 Score: 835
Period size: 343 Copynumber: 2.0 Consensus size: 338
4916462 ATATGCTGTT
* *
4916472 AATATAAATATATTTACTTTCTATTTTGTATTAACAGTACAAAAATTATAATTTATAAAATTATT
1 AATATAAACATATTTACTTTCTATTTTGTATTAACAGTACAAAAATTATAACTTATAAAATTATT
* * * *
4916537 AATTATAATATATATACTATTATTTATATAAATTTATAATATATATACTTAAAGAGAGCTTTTAA
66 AATTATAATATATATACTATTATTTATATAAACTTATAATATATAAACCTAAAGAGAGC-TTGAA
* * * * *
4916602 TATTAAAATAGTTTTGGAATCTAACTAATTTTTTTTAATTTCATGAAATTAAGAATAAATCCATA
130 GATTAAAATAGTTCTGGAACCTAACTAATTTTTTTTAATTTCATGAAATTAAGAACAAATCCAAA
* * *
4916667 TAATTAATTAAATTAATTCATGAAACTATGATTATTAATTAATTTATAATGTCTTTTAATATATA
195 TAATTAATTAAATTAATTCATGAAACTATAATAATTAATTAATTTATAATCTCTTTTAATATATA
*
4916732 TTGTCTATATATTGTGTTAATTTATAAGAAATATAATTACTATTATATATATATATAAATATTTT
260 TTCTCTATATATTGTGTTAATTTATAAGAAATATAATTAC---T-TATATATATATAAATATTTT
4916797 TAGTATATATATACTTTA
321 TAGTATATATATACTTTA
*
4916815 AATATAAACATATTTACTTTCTATTTTGTATTAACATTACAAAAATTATAACTTATAAAATTATT
1 AATATAAACATATTTACTTTCTATTTTGTATTAACAGTACAAAAATTATAACTTATAAAATTATT
*
4916880 AATTATAATATATATAC-ATTTGTTTATATAAACTTATAATATATAAACCTAAAG-GCAAG-TTG
66 AATTATAATATATATACTA-TTATTTATATAAACTTATAATATATAAACCTAAAGAG--AGCTTG
* * ** ** *
4916942 AGAGATTAGAGTAGTTCT-GAAGCCTAGTTTTTTTTTTTTATAATTTCATGTAATTAA-AGACAA
128 A-AGATTAAAATAGTTCTGGAA-CCTA-ACTAATTTTTTT-TAATTTCATGAAATTAAGA-ACAA
* * * *
4917005 ATCCAAATATTTAATTAAATTAATTCATGAAACTATAATAATTAATTACTTTGTAATCTTTTTTA
188 ATCCAAATAATTAATTAAATTAATTCATGAAACTATAATAATTAATTAATTTATAATCTCTTTTA
* * *
4917070 ATATATATATACTTTATATA-TGTTAGGTTCATTTATAAGGAATATAATTAC-TATTATATATAT
253 ATATATAT-T-CTCTATATATTG-T--GTTAATTTATAAGAAATATAATTACTTA-TATATATA-
* *
4917133 TAAAATACTTTTATTATATATATA
311 T-AAATATTTTTAGTATATATATA
4917157 TACTTTTATA
Statistics
Matches: 293, Mismatches: 33, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
342 8 0.03
343 125 0.43
344 13 0.04
345 92 0.31
346 4 0.01
347 28 0.10
349 23 0.08
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (338 bp):
AATATAAACATATTTACTTTCTATTTTGTATTAACAGTACAAAAATTATAACTTATAAAATTATT
AATTATAATATATATACTATTATTTATATAAACTTATAATATATAAACCTAAAGAGAGCTTGAAG
ATTAAAATAGTTCTGGAACCTAACTAATTTTTTTTAATTTCATGAAATTAAGAACAAATCCAAAT
AATTAATTAAATTAATTCATGAAACTATAATAATTAATTAATTTATAATCTCTTTTAATATATAT
TCTCTATATATTGTGTTAATTTATAAGAAATATAATTACTTATATATATATAAATATTTTTAGTA
TATATATACTTTA
Found at i:4917425 original size:2 final size:2
Alignment explanation
Indices: 4917414--4917451 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4917404 TGTATAAACT
4917414 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4917452 CTCTCTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4927102 original size:20 final size:20
Alignment explanation
Indices: 4927073--4927111 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4927063 ATCCTTGTGT
4927073 CTTGGATTTATT-TTTATGC
1 CTTGGATTTATTGTTTATGC
4927092 CTTGTGATTTATTGTTTATG
1 CTTG-GATTTATTGTTTATG
4927112 TTTGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.59
Consensus pattern (20 bp):
CTTGGATTTATTGTTTATGC
Found at i:4932356 original size:11 final size:11
Alignment explanation
Indices: 4932340--4932365 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4932330 TGTAGTAGAA
4932340 TATAGTAAAAT
1 TATAGTAAAAT
4932351 TATAGTAAAAT
1 TATAGTAAAAT
4932362 TATA
1 TATA
4932366 TTGTAGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
TATAGTAAAAT
Found at i:4932378 original size:16 final size:16
Alignment explanation
Indices: 4932324--4932380 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
4932314 TCAAAAAAGT
4932324 TTATATTGTAGTAGAA
1 TTATATTGTAGTAGAA
* *
4932340 TATAGTAAAATTATAGTAAAA
1 T-TA-T---ATTGTAGTAGAA
4932361 TTATATTGTAGTAGAA
1 TTATATTGTAGTAGAA
4932377 TTAT
1 TTAT
4932381 TTCTAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 15 0.47
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (16 bp):
TTATATTGTAGTAGAA
Found at i:4933587 original size:250 final size:247
Alignment explanation
Indices: 4933108--4936657 Score: 2078
Period size: 250 Copynumber: 14.4 Consensus size: 247
4933098 TATTATTATC
* * * * ** *
4933108 ACTTGTTATGTTAACTCTCACACATTTACGTTAATATTT-TAATTTTTTTA-TTCTACTTTTATA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACCTTTATA
* ** * * * * * *
4933171 AGATTTTATGTTAATTCTTACAATTTTACGTTAA-ACCTTCTCAATAGT-AACTTTT-AACTATA
65 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGA-TTTATCTAT-GTCAA-TTTTAAACTATA
* * * *
4933233 ATTATCTTTA-TCTTTATTACTCTTTATTT-AAAATAAAAATTTGA-ATATGGTTACATAC-TTT
127 ATTAT-TTTATTC-TTATTATTTTTTATTTAAAAATTAAAATTT-ATATATCGTTA-A-ACATTT
* * * ** * *
4933294 TAGCCCAATAATATAAATATAAATGCTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTA
187 TAG-TCGA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * * * * *
4933357 ACTTATTACGTTAACTTTCATACATTTACATTAAAATTTAAACTTTAGTTATTCCACCTTTATAA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* * ** * *
4933422 GTTTTTACATCAATTATTACAGTTTTACATCAAGATTTATCTATGAAAATTTTGAGCTATAATTA
66 GTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATTA
* *
4933487 TTTTATTATTATTATTTTTTATTTAAAAATTAAAATTTATATACCGTTAAACATATTTAGTCGAA
131 TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACAT-TTTAGTCG-A
* * * *
4933552 GAATATATATTTAAATATTTATTTGTCACTAAAATTAGAATTTTTTTACTTAATTG
194 -AATATAAATTTAAATATTTATTTTTCATTAAAATTAG-ATTTTTTTACTTAATTA
* * * ** ** *
4933608 ACTTGTTATGTTAACTCTCGCGTATTTATATTAAGATTTAAAATTTAATTA-TTCTACTTTTATA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACCTTTATA
* * * * * * *
4933672 AATTTTTACATCAACTATTACACTTTTACGTTAAGATTTATTTATGTCAATTTTTAACTATAATT
65 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATT
* * * *
4933737 A-TTT-TTATTATTATGTTTTATTTTAAAAAATAAAAGTTATATATCGTTTAACACA-TTTAGTC
130 ATTTTATTCTTATTATTTTTTA-TTTAAAAATTAAAATTTATATATCG-TTAA-ACATTTTAGT-
* * ** * *
4933799 CTAGAATATATATTTAAATACCTATTTTTCACTAAAATTAGATTTTTTAGTTACTTAATTG
191 CGA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGA-TTTTT--TTACTTAATTA
* * ** * * *
4933860 ACTTGTTATGTTAACTCTCACATGTTTACATTAAGATTTAAAATTTAGTTA-TTCTACTTTTATA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACCTTTATA
* * * * * * *
4933924 AGATTTTACAT-AATTTCTTACAGTTTTACTTTAAAACTTATTTATGTCAATTTTATACTATAAT
65 AGTTTTTACATCAA-TTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAAT
* *
4933988 TATTCTTA-TCTTTATTA-TTTTTATTTAAAAATTAAAATTTGTATATCTTTACATAC-TTTTAG
129 TATT-TTATTC-TTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTA-A-ACATTTTAG
* * * *
4934050 CTCGATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTA
190 -TCGA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * * *
4934110 ATTTATTACGTTAATTTTCACACATTTACGTTAAGATTTAAAATTTAACTATTTCACTTTTATAA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* * * * * *
4934175 GTTTTTACGTCAATTCTTACAGTTTTACATTAA-AGCTTATTTATATCAATTTTAAACTATAATT
66 GTTTTTACATCAATTCTTACAGTTTTACGTCAAGA-TTTATCTATGTCAATTTTAAACTATAATT
* * * * * * *
4934239 ATTTTTTTCCTTATTA-GTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTCC
130 ATTTTATT-CTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA-TTTTAGT-C
* * * * *
4934303 AAGAATATAAATTTAAATA-TT-TTTTTCAATAAAATTAGAATTTTTTATTTAATTC
192 GA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * *
4934358 ACTTATTATGTTAACTCTCACACATTT--GTTTCAGGATTTAAAATTTAATTATTTCATCTTTAT
1 ACTTATTATGTTAACTTTCACACATTTACG-TT-AAGATTTAAAATTTAATTATTTCACCTTTAT
* * * * * **********
4934421 AAGTTTTT-CATCAATTCTTATAATTTTACATCAAGATTTTTCTATGTCCATTTNNNNNNNNNNT
64 AAGTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAAT
* * * * * * *
4934485 TATTTTTATCCTTATTATTCTTTATTTAAAAAGTAAAATTTGTAGATTGTTAAATACTTTTAGTC
129 TA-TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA-TTTTAGTC
* * * **********
4934550 TGAAAATATAAATATAAATACTTATTTTTTATTANNNNNNNNNNTTTTTACTTAATTA
192 -G-AAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * * *
4934608 ATTTATTACGTTAA-TTCTCACACATTTACGTTAAGATTTAAAATTTAACTATTCCACTTTTATA
1 ACTTATTATGTTAACTT-TCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATA
* * * * *
4934672 AGTTTTTACGTCAATTCTTACAGTTTTACATTAA-AGCTTATCTATATCAATTTTAAACTATAAT
65 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGA-TTTATCTATGTCAATTTTAAACTATAAT
* * * * * * *
4934736 TATTTTTATCCTTATTA-GTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTT
129 TA-TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA-TTTTA-GT
* * * *
4934800 CCGCAAAAAGATATAAATTTAAA-ATAT-TTTTTCAATAAAATTAGA--ATTTTA-TTTATT-
191 -CG----AA-ATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * *
4934857 CCTTATTATATTAACTCTCACACATTT--GTTTCAGGATTTAAAATTTAATTATTTCATCC-TTA
1 ACTTATTATGTTAACTTTCACACATTTACG-TT-AAGATTTAAAATTTAATTATTTCA-CCTTTA
* * * * * *
4934919 TAAG---TT-CATCAATTCTTATAATTTTACATCAAGATTTTTCTATGTCCATTTTAAAGTATAA
63 TAAGTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAA
* * * * * * * *
4934980 TTATTTTTATCCTTATTATTCTTTATTTAAAAA-GAATAATATGTAGATCGTTAAATGCTTTTTG
128 TTA-TTTTATTCTTATTATTTTTTATTTAAAAATTAA-AATTTATATATCGTTAAA--CATTTTA
* * * * *
4935044 GTCTGAAATATAAATTATATATATATAATTTTTTAGCCT-AAATTA-AATTTTTTACTTAATTA
189 GTC-GAAATATAAATT-TAAATAT-TTATTTTTCA--TTAAAATTAGATTTTTTTACTTAATTA
* * * * * * *
4935106 ATTTGTTACGTTAA-TTCTCACACGTTTACGTTAAGAATTAAAATCTAATTATTTCACTTTTATA
1 ACTTATTATGTTAACTT-TCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATA
* * * *
4935170 AGTTTTTACGTCAATTCTTATAATTTTACGTTAAGATTTATCTATGTCAATTTTAAACTATAATT
65 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATT
* * *
4935235 ATTTT-TGTCTTTATTA-TATTTATTTAAAAATTAAAA--TCTGTATC------C--------CG
130 ATTTTAT-TC-TTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACATTTTAGTCG
* * * * ***
4935282 ATAATATAAATATAAATACTTATTTTTCATTAAAATTAAACTTTTTTACTTAANNN
193 A-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
****************** *
4935338 NNNNNNNNNNNNNNNNNNCACACATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* ** **********
4935403 GTTTTTATATCAATTCTTACAGTTTTACGTCAAGGCTTATCTATGTCAATNNNNNNNNNNAATTA
66 GTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATTA
* * * *
4935468 TTTTTATTCTTATTA-TTTTTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTCTA
131 -TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA-TTTTAGTC-G
********** * * * *
4935532 AGAATATAAATTTAANNNNNNNNNNTTCAATAAAATTAAATTTTTTTACTTATTTG
193 A-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* ** * *
4935588 ACCTGCTATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTT-A--A-TT-A--TTT-T-A
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* * * * *
4935644 -TCTTT--AT-AA---GT----TTTTACGTCAAGATTTTTCTATGTCCATTTTAAATTATAATTA
66 GTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATTA
* * *
4935698 TTTTAATCCTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTCAAACACTTTTAGTCCA
131 TTTT-ATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA-TTTTAGT-C-
* *
4935763 AAAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTGTTGTTTACTTAATTA
192 GAAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATT-TT-TTTACTTAATTA
* * * ** * * * *
4935821 ATTTGTTACGTTAACTCTT-ACATGTTTACATTAAGATTTAAAATTTAGTTATTCCAACTTTATA
1 ACTTATTATGTTAACT-TTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATA
*** * * *
4935885 AGTTTTTTTGTCAATTTTTACAGTTTTACGTCAAAATTTAGCTATGTCAATTTTAAA-TCATAAT
65 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACT-ATAAT
** **
4935949 TATTTTTACGCTTATTA-TTTTTATTTAAAAATTAAAA-TTATTATATTATTACATAC-TTTTAG
129 TA-TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTA-TATATCGTTA-A-ACATTTTAG
* * * * * *
4936011 CCCGATAATAT-AATATAAATACTTATTTTTTATTAAAATTAAACTTTTTTACTTAATTA
190 -TCGA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * *
4936070 ACTTATTATATTAACTCTT-ACACATTTATGTTAAGATTTAAAATTTAATTA-ATCTACCGTTAT
1 ACTTATTATGTTAACT-TTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACCTTTAT
* * * * * * * * * *
4936133 AAGTATTTACGTCAATTCTCATAGTTTTATGTCAAGGCCTTT-T-TATGTTAATTTTGAGCGATA
64 AAGTTTTTACATCAATTCTTACAGTTTTACGTCAA-G-ATTTATCTATGTCAATTTTAAACTATA
* * * ******** *
4936196 ATTATTTT-TTTTTATT-TTTTTTATTTAAAAGTAAAAATTTGA-ATNNNNNNNNNNAC-TTTCA
127 ATTATTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTT-ATAT--ATCGTTAAACATTTTA
* ** * *
4936257 GCCCGATAATATAAATACAAATTTTTATTTTTTATTAAAATTA-ATTTTTTTTACTTAATTA
189 G-TCGA-AATATAAATTTAAATATTTATTTTTCATTAAAATTAGA-TTTTTTTACTTAATTA
* * * * * * *
4936318 ATTTATTACGTTAAATTTTAAATATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* * * * * * * *
4936383 GTTCTTACATTAATTTTTATAGTTTTACATCAAGGTTTATCTATGTCAATATTGAACTATAA-T-
66 GTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATTA
********** * *
4936446 TTTTNNNNNNNNNNTTTTTTATTTAAAAATTAAAATTTATATA--GTTAACCAATTTTAGACTGA
131 TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAAC-ATTTTAGTC-GA
*
4936509 AATATAAATTTAAATA--T-TTTTT-ATTAAAATTAGATTTTTTTTACTTAATTG
194 AATATAAATTTAAATATTTATTTTTCATTAAAATTAGA-TTTTTTTACTTAATTA
* * * *
4936560 ACTTATTATGTTAACTCTCACACCTTTACGTTAAAATTTAAAATTTAATTATTTCATCTTTATAA
1 ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
* *
4936625 GTTTTGA-ATCCAATTGTTACAGTTTTACGTCAA
66 GTTTTTACAT-CAATTCTTACAGTTTTACGTCAA
4936658 AACTTAAAAA
Statistics
Matches: 2572, Mismatches: 562, Indels: 341
0.74 0.16 0.10
Matches are distributed among these distances:
229 4 0.00
230 39 0.02
231 75 0.03
232 141 0.05
233 58 0.02
234 19 0.01
236 1 0.00
237 3 0.00
238 3 0.00
240 7 0.00
241 23 0.01
242 108 0.04
243 10 0.00
244 1 0.00
245 88 0.03
246 56 0.02
247 109 0.04
248 323 0.13
249 293 0.11
250 564 0.22
251 234 0.09
252 197 0.08
253 178 0.07
254 20 0.01
255 18 0.01
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.48
Consensus pattern (247 bp):
ACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACCTTTATAA
GTTTTTACATCAATTCTTACAGTTTTACGTCAAGATTTATCTATGTCAATTTTAAACTATAATTA
TTTTATTCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACATTTTAGTCGAAA
TATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
Found at i:4934574 original size:498 final size:498
Alignment explanation
Indices: 4933117--4936629 Score: 2317
Period size: 498 Copynumber: 7.1 Consensus size: 498
4933107 CACTTGTTAT
* * * ** * *
4933117 GTTAACTCTCACACATTTACGTTAATATTT-TAATTTTTTTA-TTCTACTTTTATAAGATTTTAT
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACTTTTATAAGTTTTTAC
* * * * *
4933180 GTTAATTCTTACAATTTTACGTTAAACCTTCTCAATAGT-AACTTTT-AACTATAATTATCTTTA
65 GTCAATTCTTACAATTTTACGTTAAAGCTTATCTATA-TCAA-TTTTAAACTATAATTATTTTTA
* * * * * * * *
4933243 TCTTTATTACTCTTTATTT-AAAATAAAAATTTGAATATGGTTACATACTTTTAGCCCAATAATA
128 TCCTTATTAGT-TTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATA
* * * * * * * *
4933307 TAAATATAAATGCTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTATTACGTTAAC
192 TAAATTTAAAT-ATT-TTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAAC
* * * * * * *
4933372 TTTCATACATTTACATTAAAATTTAAACTTTAGTTATTCCACCTTTATAAGTTTTTACATCAATT
255 TCTCACACATTTACATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTT-CATCAATT
* * * ** * * **
4933437 ATTACAGTTTTACATCAAGATTTATCTATGAAAATTTTGAGCTATAATTA-TTTTATTATTATTA
319 CTTACAATTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTA
* * * * * * * *
4933501 TTTTTTATTTAAAAATTAAAATTTATATACCGTTAAACA-TATTTAGTC-GAAGAATATATATTT
384 TTCTTTATTTAAAAAGTAAAATTTGTAGATCGTTAAATACT-TTTAGTCTGAA-AATATAAATAT
* * * * * * *
4933564 AAATATTTATTTGTCACTAAAATTAGAATTTTTTTACTTAATTGACTTGTTAT
447 AAATACTTATTTTTTACTAAAATTA-AATTTTTTTACTTAATTAATTTATTAC
* * ** ** *
4933617 GTTAACTCTCGCGTATTTATATTAAGATTTAAAATTTAATTA-TTCTACTTTTATAAATTTTTAC
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACTTTTATAAGTTTTTAC
* * * * * * * *
4933681 ATCAACTATTACACTTTTACGTT-AAGATTTATTTATGTCAATTTTTAACTATAATTATTTTTA-
65 GTCAATTCTTACAATTTTACGTTAAAG-CTTATCTATATCAATTTTAAACTATAATTATTTTTAT
* * * * * * * *
4933744 --TTATTATGTTTTATTTTAAAAAATAAAAGTTATATATCGTTTAACACATTTAGTCCTAGAATA
129 CCTTATTA-GTTTTA-TTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATA
* * * * *
4933807 TATATTTAAATACCTATTTTTCACTAAAATTAG-ATTTTTTAGTTACTTAATTGACTTGTTATGT
192 TAAATTTAAATA--TTTTTTTCAATAAAATTAGAATTTTTTA--T--TTAATTCACTTATTATGT
** * *
4933871 TAACTCTCACATGTTTACATTAAGATTTAAAATTTAGTTA-TTC-TACTTTTATAAGATTTTACA
251 TAACTCTCACACATTTACATTAAGATTTAAAATTTAATTATTTCAT-C-TTTATAAG-TTTTTCA
* * * * * * *
4933934 T-AATTTCTTACAGTTTTACTTTAAAACTTATT-TATGTCAATTTTATACTATAATTATTCTTAT
313 TCAA-TTCTTACAATTTTACATCAAGA-TTTTTCTATGTCAATTTTAAACTATAATTATTTTTAT
* * * * * *
4933997 CTTTATTATT-TTTATTTAAAAATTAAAATTTGTATATCTTTACATACTTTTAG-CTCGATAATA
376 CCTTATTATTCTTTATTTAAAAAGTAAAATTTGTAGATCGTTAAATACTTTTAGTCT-GAAAATA
*
4934060 TAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
440 TAAATATAAATACTTATTTTTTACTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
* *
4934119 GTTAATTTTCACACATTTACGTTAAGATTTAAAATTTAACTATTTCACTTTTATAAGTTTTTACG
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACG
* * * *
4934184 TCAATTCTTACAGTTTTACATTAAAGCTTATTTATATCAATTTTAAACTATAATTATTTTTTTCC
66 TCAATTCTTACAATTTTACGTTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCC
* *
4934249 TTATTAGTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTCCAAGAATATAAA
131 TTATTAGTTTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATATAAA
4934314 TTTAAATATTTTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAACTCTCAC
196 TTTAAATATTTTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAACTCTCAC
** * *
4934379 ACATTT-GTTTCAGGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTCATCAATTCTTATA
261 ACATTTACATT-AAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTCATCAATTCTTACA
* **********
4934443 ATTTTACATCAAGATTTTTCTATGTCCATTTNNNNNNNNNNTTATTTTTATCCTTATTATTCTTT
325 ATTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTATTCTTT
*
4934508 ATTTAAAAAGTAAAATTTGTAGATTGTTAAATACTTTTAGTCTGAAAATATAAATATAAATACTT
390 ATTTAAAAAGTAAAATTTGTAGATCGTTAAATACTTTTAGTCTGAAAATATAAATATAAATACTT
* **********
4934573 ATTTTTTATTANNNNNNNNNNTTTTTACTTAATTAATTTATTAC
455 ATTTTTTACTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
* *
4934617 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAACTATTCCACTTTTATAAGTTTTTACG
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACG
* *
4934682 TCAATTCTTACAGTTTTACATTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCC
66 TCAATTCTTACAATTTTACGTTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCC
* * *
4934747 TTATTAGTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTTCCGCAAAAAGAT
131 TTATTAGTTTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTA-GT-C-C-AAGA-AT
*
4934812 ATAAATTTAAA-ATATTTTTTCAATAAAATTAGAA--TTTTATTT-ATTC-CTTATTATATTAAC
191 ATAAATTTAAATAT-TTTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAAC
** * *
4934872 TCTCACACATTT-GTTTCAGGATTTAAAATTTAATTATTTCATCCTTATAAG---TTCATCAATT
255 TCTCACACATTTACATT-AAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTCATCAATT
* * *
4934933 CTTATAATTTTACATCAAGATTTTTCTATGTCCATTTTAAAGTATAATTATTTTTATCCTTATTA
319 CTTACAATTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTA
* * *
4934998 TTCTTTATTTAAAAAG-AATAATATGTAGATCGTTAAATGCTTTTTGGTCTG-AAATATAAATTA
384 TTCTTTATTTAAAAAGTAA-AATTTGTAGATCGTTAAATAC-TTTTAGTCTGAAAATATAAA-TA
* *
4935061 TATATATA-TAATTTTTTAGCCT-AAATTAAA-TTTTTTACTTAATTAATTTGTTAC
446 TA-A-ATACTTATTTTTTA--CTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
* * *
4935115 GTTAATTCTCACACGTTTACGTTAAGAATTAAAATCTAATTATTTCACTTTTATAAGTTTTTACG
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACG
* * * *
4935180 TCAATTCTTATAATTTTACGTT-AAGATTTATCTATGTCAATTTTAAACTATAATTATTTTTGTC
66 TCAATTCTTACAATTTTACGTTAAAG-CTTATCTATATCAATTTTAAACTATAATTATTTTTATC
* * *** *
4935244 TTTATTA-TATTTATTTAAAAATTAAAATCTGTATCCCG----ATA---ATA-T---A-AATATA
130 CTTATTAGT-TTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATATA
* * * * *********************
4935296 AA--T-ACT-TATTTTTCATTAAAATTA-AACTTTTTTACTTAANNNNNNNNNNNNNNNNNNNNN
194 AATTTAAATATTTTTTTCAATAAAATTAGAA-TTTTTTATTTAATTCACTTATTATGTTAACTCT
* * * *
4935356 CACACATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAAGTTTTTATATCAATTCTT
258 CACACATTTACATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTT-CATCAATTCTT
* * ** * ********** *
4935421 ACAGTTTTACGTCAAGGCTTATCTATGTCAATNNNNNNNNNNAATTATTTTTATTCTTATTATT-
322 ACAATTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTATTC
* * * * * * **
4935485 TTTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTCT-AAGAATATAAATTTAANN
387 TTTATTTAAAAAGTAAAATTTGTAGATCGTTAAATACTTTTAGTCTGAA-AATATAAATATAAAT
******** * * * * ** ** *
4935549 NNNNNNNNTTCAATAAAATTAAATTTTTTTACTTATTTGACCTGCTAT
451 ACTTATTTTTTACTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
* * *
4935597 GTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAATTATTTTA-TCTTTATAAGTTTTTAC
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACT-TTTATAAGTTTTTAC
* * * * *
4935661 G--------T-CAA---GA--TT-----TT-TCTATGTCCATTTTAAATTATAATTATTTTAATC
65 GTCAATTCTTACAATTTTACGTTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATC
* * * * * *
4935706 CTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTCAAACACTTTTAGTCCAAAAATATA
130 CTTATTAGT-TTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATATA
* * * * * * *
4935771 AATTTAAATATTTATTTTTCACTAAAATTAGATTGTTGTTTACTTAATTAATTTGTTACGTTAAC
194 AATTTAAATA-TT-TTTTTCAATAAAATTAGAAT-TT-TTTATTTAATTCACTTATTATGTTAAC
* ** * * * **
4935836 TCTTACATGTTTACATTAAGATTTAAAATTTAGTTATTCCAACTTTATAAGTTTTTTTGTCAATT
255 TCTCACACATTTACATTAAGATTTAAAATTTAATTATTTCATCTTTATAAG-TTTTTCATCAATT
* * * * **
4935901 TTTACAGTTTTACGTCAAAATTTAGCTATGTCAATTTTAAA-TCATAATTATTTTTA-CGCTTAT
319 CTTACAATTTTACATCAAGATTTTTCTATGTCAATTTTAAACT-ATAATTATTTTTATC-CTTAT
* * ** * * * *
4935964 TATT-TTTATTTAAAAATTAAAATTAT-TATATTATTACATACTTTTAGCCCGATAATAT-AATA
382 TATTCTTTATTTAAAAAGTAAAATT-TGTAGATCGTTAAATACTTTTAGTCTGAAAATATAAATA
* * * *
4936026 TAAATACTTATTTTTTATTAAAATTAAACTTTTTTACTTAATTAACTTATTAT
446 TAAATACTTATTTTTTACTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
* * * * * ** *
4936079 ATTAACTCTTACACATTTATGTTAAGATTTAAAATTTAATTA-ATCTACCGTTATAAGTATTTAC
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTC-ACTTTTATAAGTTTTTAC
* * * * * * * * * * * *
4936143 GTCAATTCTCATAGTTTTATGTCAAGGCCTT-TTTATGTTAATTTTGAGCGATAATTATTTTT-T
65 GTCAATTCTTACAATTTTACGTTAAAG-CTTATCTATATCAATTTTAAACTATAATTATTTTTAT
* ** * * * ********** * * * *
4936206 -TTTATTTTTTTTATTTAAAAGTAAAAATTTGAATNNNNNNNNNNACTTTCAGCCCGATAATATA
129 CCTTATTAGTTTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATATA
** * * * * * * * * *
4936270 AATACAAATTTTTATTTTTTATTAAAATTA-ATTTTTTTTACTTAATTAATTTATTACGTTAAAT
194 AATTTAAA-TATT-TTTTTCAATAAAATTAGA-ATTTTTTATTTAATTCACTTATTATGTTAACT
* * * * * * * * * *
4936334 TTTAAATATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAAGTTCTTACATTAATTT
256 CTCACACATTTACATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTT-TTTCATCAATTC
* * * * * * **********
4936399 TTATAGTTTTACATCAAGGTTTATCTATGTCAATATTGAACTATAATT-TTTNNNNNNNNNNT-T
320 TTACAATTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTAT
* * * ** * * *
4936462 T-TTTATTTAAAAATTAAAA-TT-TATATAGTTAACCAATTTTAGACTG-AAATATAAAT-TTAA
385 TCTTTATTTAAAAAGTAAAATTTGTAGATCGTTAAATACTTTTAGTCTGAAAATATAAATATAAA
* * * * *
4936522 -A--TATTTTTTATTAAAATTAGATTTTTTTTACTTAATTGACTTATTAT
450 TACTTATTTTTTACTAAAATTA-AATTTTTTTACTTAATTAATTTATTAC
* * *
4936569 GTTAACTCTCACACCTTTACGTTAAAATTTAAAATTTAATTATTTCA-TCTTTATAAGTTTT
1 GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACT-TTTATAAGTTTT
4936630 GAATCCAATT
Statistics
Matches: 2412, Mismatches: 475, Indels: 262
0.77 0.15 0.08
Matches are distributed among these distances:
462 36 0.01
463 28 0.01
467 2 0.00
468 2 0.00
470 3 0.00
471 1 0.00
473 2 0.00
474 2 0.00
475 8 0.00
476 2 0.00
477 16 0.01
478 4 0.00
479 8 0.00
480 3 0.00
481 72 0.03
482 178 0.07
483 164 0.07
484 45 0.02
485 58 0.02
489 19 0.01
490 72 0.03
491 6 0.00
492 8 0.00
493 21 0.01
494 5 0.00
495 22 0.01
496 119 0.05
497 188 0.08
498 517 0.21
499 147 0.06
500 103 0.04
501 96 0.04
502 168 0.07
503 252 0.10
504 29 0.01
505 6 0.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.48
Consensus pattern (498 bp):
GTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACG
TCAATTCTTACAATTTTACGTTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCC
TTATTAGTTTTATTTAAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATATAAA
TTTAAATATTTTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAACTCTCAC
ACATTTACATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTCATCAATTCTTACAA
TTTTACATCAAGATTTTTCTATGTCAATTTTAAACTATAATTATTTTTATCCTTATTATTCTTTA
TTTAAAAAGTAAAATTTGTAGATCGTTAAATACTTTTAGTCTGAAAATATAAATATAAATACTTA
TTTTTTACTAAAATTAAATTTTTTTACTTAATTAATTTATTAC
Found at i:4934816 original size:753 final size:747
Alignment explanation
Indices: 4933108--4936629 Score: 2230
Period size: 753 Copynumber: 4.8 Consensus size: 747
4933098 TATTATTATC
* * * * **
4933108 ACTTGTTATGTTAACTCTCACACATTTACGTTAATATTT-TAATTTTTTTATTCTACTTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCTACTTTTATAA
* * * * * *
4933172 GATTTTATGTTAATTCTTACAATTTTACGTTAAACCTTCTCAATAGT-AACTTTT-AACTATAAT
66 GATTTTACG-TAATTCTTACAGTTTTACATTAAAACTTATCTATA-TCAA-TTTTAAACTATAAT
* * * * *
4933235 TATCTTTATCTTTATTACTCTTTATTT-AAAATAAAAATTTGAATATGGTTACATACTTTTAGCC
128 TATTTTTATCTTTATTACT-TTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTATCC
* * *
4933299 -CAATAATATAAATATAAATGCTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTAT
192 GCAATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAA-TTAT
* * * * * * *
4933363 TACGTTAACTTTCATACATTTACATTAAAATTTAAACTTTAGTTATTCCACCTTTATAAGTTTTT
256 TACGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTT
* * * * * *
4933428 ACATCAATTATTACAGTTTTACATCAAGATTTATCTATGA-AAATTTTGAGCTATAATTATTTTA
321 ACATCAATTCTTACAGTTTTACATCAAGA-TTATTTAT-ATCAATTTTAAACTATAATTATTTTT
* * ** * * *
4933492 TT-ATTATTATTTTTTATTTAAAAATTAAAATTTATATACCGTTAAACA-TATTTAGTCGAAGAA
384 TTCCTTATTA-TTTTTATTTAAAAATTAAAATTTGTATGTCGTTAAATACT-TTTATTCCAAGAA
* *
4933555 TATATATTTAAATATTTATTTGTCACTAAAATTAGAATTTTTTTACTTAATTGACTTGTTATGTT
447 TATAAATTTAAATATTT-TTT-TCACTAAAATTAGAA-TTTTTTACTTAATTAACTTGTTATGTT
* ** * *
4933620 AACTCTCGCGTATTTATATTAAGATTTAAAATTTAATTA-TTC-TACTTTTATAAATTTTTACAT
509 AACTCTCACACATTTGT-TTAAGATTTAAAATTTAATTATTTCAT-CTTTTATAAGTTTTTACAT
* * * *
4933683 CAACTATTACACTTTTACGTTAAGATTTATT-TATGTCAATTTTTAACTATAATTATTTTTATTA
572 CAATTCTTATAATTTTACGTTAAGATTT-TTCTATGTCAATTTTTAACTATAATTATTTTTATTA
* * * *
4933747 TTATGTTTTATTTTAAAAAATAAAAGTTATATATCGTTTAACACATTTAGTCCTAGAATATATAT
636 TTATGTTTTATTTTAAAAAATAAAAGTTATAGATCGTTAAACACATTTAGTCCTAAAATATAAAT
* *
4933812 TTAAATACCTATTTTTCACTAAAATTAGATTTTTTAGTTACTTAATTG
701 ATAAATACCTATTTTTCACTAAAATTAGATTTTTTA-TTACTTAATTA
* * ** * *
4933860 ACTTGTTATGTTAACTCTCACATGTTTACATTAAGATTTAAAATTTAGTTATTCTACTTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCTACTTTTATAA
* * * * *
4933925 GATTTTACATAATTTCTTACAGTTTTACTTTAAAACTTATTTATGTCAATTTTATACTATAATTA
66 GATTTTACGTAA-TTCTTACAGTTTTACATTAAAACTTATCTATATCAATTTTAAACTATAATTA
* * *
4933990 TTCTTATCTTTATTATTTTTATTTAAAAATTAAAATTTGTATATCT-TTACATACTTTTAGCTCG
130 TTTTTATCTTTATTACTTTTATTTAAAAATTAAAATTTGTATAT-TGTTACATACTTTTATC-CG
4934054 --ATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAATTTATT
193 CAATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAA-TTATT
* *
4934117 ACGTTAATTTTCACACATTTACGTTAAGATTTAAAATTTAACTATTTCACTTTTATAAGTTTTTA
257 ACGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTA
* * *
4934182 CGTCAATTCTTACAGTTTTACATTAAAGCTTATTTATATCAATTTTAAACTATAATTATTTTTTT
322 CATCAATTCTTACAGTTTTACA-TCAAGATTATTTATATCAATTTTAAACTATAATTATTTTTTT
* *
4934247 CCTTATTAGTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTCCAAGAATATA
386 CCTTATTATTTTTATTTAAAAATTAAAATTTGTATGTCGTTAAATACTTTTATTCCAAGAATATA
* * * *
4934312 AATTTAAATATTTTTTTCAATAAAATTAGAATTTTTTATTTAATTCACTTATTATGTTAACTCTC
451 AATTTAAATATTTTTTTCACTAAAATTAGAATTTTTTACTTAATTAACTTGTTATGTTAACTCTC
*
4934377 ACACATTTGTTTCAGGATTTAAAATTTAATTATTTCATC-TTTATAAGTTTTT-CATCAATTCTT
516 ACACATTTGTTT-AAGATTTAAAATTTAATTATTTCATCTTTTATAAGTTTTTACATCAATTCTT
* * * **********
4934440 ATAATTTTACATCAAGATTTTTCTATGTCCATTTNNNNNNNNNNTTATTTTTATCCTTATTAT-T
580 ATAATTTTACGTTAAGATTTTTCTATGTCAATTTTTAACTATAATTATTTTTA---TTATTATGT
* * * * * *
4934504 CTTTA-TTTAAAAAGTAAAATTTGTAGATTGTTAAATACTTTTAGT-CTGAAAATATAAATATAA
642 -TTTATTTTAAAAAATAAAAGTTATAGATCGTTAAACACATTTAGTCCT-AAAATATAAATATAA
* * * **********
4934567 ATACTTATTTTTTA-TTANNNNNNNNNNTTT-TTACTTAATTA
705 ATACCTATTTTTCACTAAAATTAGATTTTTTATTACTTAATTA
* * * *
4934608 ATTTATTACGTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAACTATTCCACTTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCTACTTTTATAA
* *
4934673 GTTTTTACGTCAATTCTTACAGTTTTACATTAAAGCTTATCTATATCAATTTTAAACTATAATTA
66 GATTTTACGT-AATTCTTACAGTTTTACATTAAAACTTATCTATATCAATTTTAAACTATAATTA
* * * *
4934738 TTTTTATCCTTATTAGTTTTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTTCCG
130 TTTTTATCTTTATTACTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTA--TCCG
* * * **
4934803 CAAAAAGATATAAATTTAAA-A--TATTTTTTCAATAAAATTAGAATTTTATTTA-TTCCTT-AT
193 C-AATA-ATATAAATATAAATACTTATTTTTT-ATTAAAATTA-AATTTT-TTTACTTAATTAAT
* * *
4934863 TA-TA--TTAACTCTCACACATTT--GTTTCAGGATTTAAAATTTAATTATTTCA-TCCTTATAA
253 TATTACGTTAACTTTCACACATTTACG-TT-AAGATTTAAAATTTAATTATTTCACT-TTTATAA
* * * * * *
4934922 G---TT-CATCAATTCTTATAATTTTACATCAAGATTTTTCTATGTCCATTTTAAAGTATAATTA
315 GTTTTTACATCAATTCTTACAGTTTTACATCAAGATTATT-TATATCAATTTTAAACTATAATTA
* * * *
4934983 TTTTTATCCTTATTATTCTTTATTTAAAAA-GAATAATATGTA-GATCGTTAAATGCTTTT-TGG
379 TTTTTTTCCTTATTATT-TTTATTTAAAAATTAA-AATTTGTATG-TCGTTAAATACTTTTAT--
**
4935045 TCTGA-AATATAAATTATATATATATAATTTTTT-AGCCT-AAATTA-AATTTTTTACTTAATTA
439 TCCAAGAATATAAATT-TA-A-ATAT--TTTTTTCA--CTAAAATTAGAATTTTTTACTTAATTA
* * * * * *
4935106 ATTTGTTACGTTAATTCTCACACGTTTACG-TTAAGAATTAAAATCTAATTATTTCA-CTTTTAT
497 ACTTGTTATGTTAACTCTCACACATTT--GTTTAAGATTTAAAATTTAATTATTTCATCTTTTAT
* * *
4935169 AAGTTTTTACGTCAATTCTTATAATTTTACGTTAAGATTTATCTATGTCAATTTTAAACTATAAT
560 AAGTTTTTACATCAATTCTTATAATTTTACGTTAAGATTTTTCTATGTCAATTTTTAACTATAAT
* * * *
4935234 TATTTTTGTCTTTATTAT-ATTTA-TTTAAAAATTAAAA--TCT-GTATC------C-C-----G
625 TA-TTTT-T-ATTATTATGTTTTATTTTAAAAAATAAAAGTTATAG-ATCGTTAAACACATTTAG
* * * ** ***
4935282 ----ATAATATAAATATAAATACTTATTTTTCATTAAAATTA-AACTTTT-TTACTTAANNN
686 TCCTAAAATATAAATATAAATACCTATTTTTCACTAAAATTAGATTTTTTATTACTTAATTA
****************** * *
4935338 NNNNNNNNNNNNNNNNNNCACACATTTACGTTAAGATTTAAAATTTAGTTATT-TCACCTTTATA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCT-ACTTTTATA
* ** * * ** * **********
4935402 AGTTTTTATATCAATTCTTACAGTTTTACGTCAAGGCTTATCTATGTCAATNNNNNNNNNNAATT
65 AGATTTTACGT-AATTCTTACAGTTTTACATTAAAACTTATCTATATCAATTTTAAACTATAATT
* * ** * *
4935467 ATTTTTAT-TCTTATTATTTTTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTC-
129 ATTTTTATCT-TTATTACTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTATCCG
* * * ********** * * * ** **
4935530 TAAGAATATAAATTTAANNNNNNNNNNTTCAATAAAATTAAATTTTTTTACTTATTTGACCTGCT
193 CAATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATT-AATTATT
* * * *
4935595 ATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAATTATTTTA-TCTTTATAAGTTTTT
257 ACGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACT-TTTATAAGTTTTT
* * * * * **
4935659 ACGTC-A-----AGA-TTTT---TC---------TATGTCCATTTTAAATTATAATTATTTTAAT
321 ACATCAATTCTTACAGTTTTACATCAAGATTATTTATATCAATTTTAAACTATAATTATTTTTTT
* * * * * *
4935705 CCTTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTCAAACACTTTTAGTCCAAAAATAT
386 CCTTATTATT-TTTATTTAAAAATTAAAATTTGTATGTCGTTAAATACTTTTATTCCAAGAATAT
* * *
4935770 AAATTTAAATATTTATTTTTCACTAAAATTAGATTGTTGTTTACTTAATTAATTTGTTACGTTAA
450 AAATTTAAATA-TT-TTTTTCACTAAAATTAGAAT-TT-TTTACTTAATTAACTTGTTATGTTAA
* ** ** * * * ***
4935835 CTCTTACATGTTTACATTAAGATTTAAAATTTAGTTATTCCAAC-TTTATAAGTTTTTTTGTCAA
511 CTCTCACACATTT-GTTTAAGATTTAAAATTTAATTATTTCATCTTTTATAAGTTTTTACATCAA
* * * * * ** *
4935899 TTTTTACAGTTTTACGTCAAAATTTAGCTATGTCAA-TTTTAAATCATAATTATTTTTACGCTTA
575 TTCTTATAATTTTACGTTAAGATTTTTCTATGTCAATTTTTAACT-ATAATTATTTTTA---TTA
* * ** * * * * * *
4935963 TTAT-TTTTA-TTTAAAAATTAAAA-TTATTATATTATTACATACTTTTAGCCCGATAATAT-AA
636 TTATGTTTTATTTTAAAAAATAAAAGTTA-TAGATCGTTAAACACATTTAGTCCTAAAATATAAA
* * * **
4936024 TATAAATACTTATTTTTTATTAAAATTA-AACTTTT-TTACTTAATTA
700 TATAAATACCTATTTTTCACTAAAATTAGATTTTTTATTACTTAATTA
** * * * **
4936070 ACTTATTATATTAACTCTTACACATTTATGTTAAGATTTAAAATTTAATTAATCTACCGTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCTACTTTTATAA
* * ** * ** * * * * * *
4936135 G-TATTTACGTCAATTCTCATAGTTTTATGTCAAGGCCTT-TTTATGTTAATTTTGAGCGATAAT
66 GAT-TTTACGT-AATTCTTACAGTTTTACATTAA-AACTTATCTATATCAATTTTAAACTATAAT
** * * * ********** * *
4936198 TATTTTT-T-TTTATTTTTTTTATTTAAAAGTAAAAATTTGAATNNNNNNNNNNACTTTCAGCC-
128 TATTTTTATCTTTATTACTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTATCCG
* * ** *
4936260 CGATAATATAAATACAAATTTTTATTTTTTATTAAAATTAATTTTTTTTACTTAATTAATTTATT
193 CAATAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAA-TTATT
* * * * * * *
4936325 ACGTTAAATTTTAAATATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAAGTTCTTA
257 ACGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTA
* * * * * * * * ****
4936390 CATTAATTTTTATAGTTTTACATCAAGGTTTATCTATGTCAATATTGAACTATAATT-TTTNNNN
322 CATCAATTCTTACAGTTTTACATCAA-GATTATTTATATCAATTTTAAACTATAATTATTTTTTT
****** * * ** * ** **
4936454 NNNNNNT-TTTTTATTTAAAAATTAAAA-TT-TATATAGTTAACCAATTTTAGACTGA-AATATA
386 CCTTATTATTTTTATTTAAAAATTAAAATTTGTATGTCGTTAAATACTTTTATTCCAAGAATATA
* * * *
4936515 AATTTAAATA-TTTTTT-ATTAAAATTAGATTTTTTTTACTTAATTGACTTATTATGTTAACTCT
451 AATTTAAATATTTTTTTCACTAAAATTAGA-ATTTTTTACTTAATTAACTTGTTATGTTAACTCT
* *
4936578 CACACCTTTACG-TTAAAATTTAAAATTTAATTATTTCATC-TTTATAAGTTTT
515 CACACATTT--GTTTAAGATTTAAAATTTAATTATTTCATCTTTTATAAGTTTT
4936630 GAATCCAATT
Statistics
Matches: 2191, Mismatches: 442, Indels: 287
0.75 0.15 0.10
Matches are distributed among these distances:
711 3 0.00
712 14 0.01
713 6 0.00
714 17 0.01
715 218 0.10
716 4 0.00
717 3 0.00
724 1 0.00
725 18 0.01
726 13 0.01
727 10 0.00
728 9 0.00
729 6 0.00
730 311 0.14
731 54 0.02
732 131 0.06
733 13 0.01
734 4 0.00
735 3 0.00
736 2 0.00
737 4 0.00
739 69 0.03
740 15 0.01
741 7 0.00
742 9 0.00
743 59 0.03
744 60 0.03
745 26 0.01
746 10 0.00
747 68 0.03
748 265 0.12
749 120 0.05
750 111 0.05
751 86 0.04
752 79 0.04
753 351 0.16
754 12 0.01
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.48
Consensus pattern (747 bp):
ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCTACTTTTATAA
GATTTTACGTAATTCTTACAGTTTTACATTAAAACTTATCTATATCAATTTTAAACTATAATTAT
TTTTATCTTTATTACTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTATCCGCAA
TAATATAAATATAAATACTTATTTTTTATTAAAATTAAATTTTTTTACTTAATTAATTATTACGT
TAACTTTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACATC
AATTCTTACAGTTTTACATCAAGATTATTTATATCAATTTTAAACTATAATTATTTTTTTCCTTA
TTATTTTTATTTAAAAATTAAAATTTGTATGTCGTTAAATACTTTTATTCCAAGAATATAAATTT
AAATATTTTTTTCACTAAAATTAGAATTTTTTACTTAATTAACTTGTTATGTTAACTCTCACACA
TTTGTTTAAGATTTAAAATTTAATTATTTCATCTTTTATAAGTTTTTACATCAATTCTTATAATT
TTACGTTAAGATTTTTCTATGTCAATTTTTAACTATAATTATTTTTATTATTATGTTTTATTTTA
AAAAATAAAAGTTATAGATCGTTAAACACATTTAGTCCTAAAATATAAATATAAATACCTATTTT
TCACTAAAATTAGATTTTTTATTACTTAATTA
Found at i:4935104 original size:17 final size:16
Alignment explanation
Indices: 4935069--4935121 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
4935059 TATATATATA
*
4935069 TAATTTTTTAGCCTAAAT
1 TAATTTTTTA--CTTAAT
4935087 TAAATTTTTTACTTAAT
1 T-AATTTTTTACTTAAT
*
4935104 TAATTTGTTACGTTAAT
1 TAATTTTTTAC-TTAAT
4935121 T
1 T
4935122 CTCACACGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 9 0.29
17 12 0.39
18 1 0.03
19 9 0.29
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.55
Consensus pattern (16 bp):
TAATTTTTTACTTAAT
Found at i:4935470 original size:730 final size:690
Alignment explanation
Indices: 4934626--4935986 Score: 1384
Period size: 715 Copynumber: 1.9 Consensus size: 690
4934616 CGTTAATTCT
* *
4934626 CACACATTTACGTTAAGATTTAAAATTTAACTATTCCACTTTTATAAGTTTTTACGTCAATTCTT
1 CACACATTTACGTTAAGATTTAAAATTTAACTATTCCACCTTTATAAGTTTTTACATCAATTCTT
*
4934691 ACAGTTTTACATTAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCCTTATTAGTT
66 ACAGTTTTACATCAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCCTTATTAGTT
* * **
4934756 TTATTTAAAAATTAAAATTTGTATGTTGTTAAATACTTTTATTTCCGCAAAAAGATATAAATTT-
131 TTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTA-TT---CAAAAA-ATATAAATTTA
*
4934820 AAAATATTTTTTCAATAAAATTAGAATTTTATTTA-TTCCTT-A-T-TATATTAACTCTCACACA
191 AAAATATTTTTTCAATAAAATTA-AATTTT-TTTACTTACTTGACTCTATATTAACTCTCACACA
* *
4934881 TTTGT-TTCAGGATTTAAAATTTAATTATTTCATCCTTATAAGTTCATCAATTCTTATAATTTTA
254 TTTATGTT-AAGATTTAAAATTTAATTATTTCAT-C---T---TT-AT-AA-----AT--TTTTA
*
4934945 CATCAAGATTTTTCTATGTCCATTTTAAAGTATAATTATTTTTATCCTTATTATTCTTTATTTAA
302 CATCAAGATTTTTCTATGTCCATTTTAAAGTATAATTATTTTAATCCTTATTATTCTTTATTTAA
* * ** * ** *
4935010 AAA-GAATAATATGTAGATCGTTAAATGCTTTTTGGT-CTGAAATATAAATTATATATATATAAT
367 AAATGAA-AATATATAGATCGTCAAACAC-TTTTAGTCCAAAAATATAAATT-TAAATAT-TAAT
* *
4935073 TTTTTAGCCT-AAATTA-AAT-TT-TTTACTTAATTAATTTGTTACGTTAATTCTCACACGTTTA
428 TTTTCA--CTAAAATTAGAATGTTGTTTACTTAATTAATTTGTTACGTTAACTCTCACACGTTTA
* * *
4935134 CGTTAAGAATTAAAATCTAATTATTTC-ACTTTTATAAGTTTTTACGTCAATTCTTATAATTTTA
491 CATTAAGAATTAAAATCTAATTATTCCAAC-TTTATAAGTTTTTACGTCAATTCTTACAATTTTA
* * *
4935198 CGTTAAGATTTATCTATGTCAATTTTAAA-CTATAATTATTTTT-GTCTTTATTATATTTATTTA
555 CGTCAAAATTTAGCTATGTCAATTTTAAATC-ATAATTATTTTTAG-C-TTATTATATTTATTTA
4935261 AAAATTAAAATCTGTATCCCGATAATATAAATATAAATACTTATTTTTCATTAAAATTAAACTTT
617 AAAATTAAAATCTGTATCCCGATAATATAAATATAAATACTTATTTTTCATTAAAATTAAACTTT
4935326 TTTACTTAA
682 TTTACTTAA
** *
4935335 NNNNNNNNNNNNNNNNNNNNNCACACATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTA
1 ---------------------CACACATTTACGTTAAGATTTAAAATTTAACTATTCCACCTTTA
* * * * **********
4935400 TAAGTTTTTATATCAATTCTTACAGTTTTACGTCAAGGCTTATCTATGTCAATNNNNNNNNNNAA
45 TAAGTTTTTACATCAATTCTTACAGTTTTACATCAAAGCTTATCTATATCAATTTTAAACTATAA
* *
4935465 TTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTC
110 TTATTTTTATCCTTATTAGTTTTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTC
* * ********* *
4935530 TAAGAATATAAATTTAANNNNNNNNNNTTCAATAAAATTAAATTTTTTTACTTATTTGACCTGCT
175 AAAAAATATAAATTTAA-AAATATTTTTTCAATAAAATTAAATTTTTTTACTTACTTGA-CT-CT
* * *
4935595 ATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAATTATTTTATCTTTATAAGTTTTTA
237 ATATTAACTCTCACACATTTATGTTAAGATTTAAAATTTAATTATTTCATCTTTATAAATTTTTA
* *
4935660 CGTCAAGATTTTTCTATGTCCATTTTAAATTATAATTATTTTAATCCTTATTATTCTTTATTTAA
302 CATCAAGATTTTTCTATGTCCATTTTAAAGTATAATTATTTTAATCCTTATTATTCTTTATTTAA
* * * *
4935725 AAATTAAAATTTATATATCGTCAAACACTTTTAGTCCAAAAATATAAATTTAAATATTTATTTTT
367 AAATGAAAATATATAGATCGTCAAACACTTTTAGTCCAAAAATATAAATTTAAATATTAATTTTT
* * *
4935790 CACTAAAATTAGATTGTTGTTTACTTAATTAATTTGTTACGTTAACTCTTACATGTTTACATTAA
432 CACTAAAATTAGAATGTTGTTTACTTAATTAATTTGTTACGTTAACTCTCACACGTTTACATTAA
* * * ** * *
4935855 GATTTAAAATTTAGTTATTCCAACTTTATAAGTTTTTTTGTCAATTTTTACAGTTTTACGTCAAA
497 GAATTAAAATCTAATTATTCCAACTTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAA
*
4935920 ATTTAGCTATGTCAATTTTAAATCATAATTATTTTTACGCTTATTATTTTTATTTAAAAATTAAA
562 ATTTAGCTATGTCAATTTTAAATCATAATTATTTTTA-GCTTATTATATTTATTTAAAAATTAAA
4935985 AT
626 AT
4935987 TATTATATTA
Statistics
Matches: 534, Mismatches: 78, Indels: 53
0.80 0.12 0.08
Matches are distributed among these distances:
711 2 0.00
712 6 0.01
713 10 0.02
714 14 0.03
715 249 0.47
716 6 0.01
717 2 0.00
722 2 0.00
723 2 0.00
724 2 0.00
725 14 0.03
726 15 0.03
727 15 0.03
729 3 0.01
730 146 0.27
731 44 0.08
732 2 0.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.47
Consensus pattern (690 bp):
CACACATTTACGTTAAGATTTAAAATTTAACTATTCCACCTTTATAAGTTTTTACATCAATTCTT
ACAGTTTTACATCAAAGCTTATCTATATCAATTTTAAACTATAATTATTTTTATCCTTATTAGTT
TTATTTAAAAATTAAAATTTATATATCATTAAATACTTTTATTCAAAAAATATAAATTTAAAAAT
ATTTTTTCAATAAAATTAAATTTTTTTACTTACTTGACTCTATATTAACTCTCACACATTTATGT
TAAGATTTAAAATTTAATTATTTCATCTTTATAAATTTTTACATCAAGATTTTTCTATGTCCATT
TTAAAGTATAATTATTTTAATCCTTATTATTCTTTATTTAAAAATGAAAATATATAGATCGTCAA
ACACTTTTAGTCCAAAAATATAAATTTAAATATTAATTTTTCACTAAAATTAGAATGTTGTTTAC
TTAATTAATTTGTTACGTTAACTCTCACACGTTTACATTAAGAATTAAAATCTAATTATTCCAAC
TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAAATTTAGCTATGTCAATTTTAAATC
ATAATTATTTTTAGCTTATTATATTTATTTAAAAATTAAAATCTGTATCCCGATAATATAAATAT
AAATACTTATTTTTCATTAAAATTAAACTTTTTTACTTAA
Found at i:4936135 original size:249 final size:253
Alignment explanation
Indices: 4935655--4936136 Score: 607
Period size: 249 Copynumber: 1.9 Consensus size: 253
4935645 CTTTATAAGT
* ** * *
4935655 TTTTACGTCAAGATTTTTCTATGTCCATTTTAAATTATAATTATTTTAATCCTTATTATTCTTTA
1 TTTTACGTCAAAATTTAGCTATGTCAATTTTAAATCATAATTATTTTAATCCTTATTATTCTTTA
* * * *
4935720 TTTAAAAATTAAAATTTATATATCGTCAAACACTTTTAGTCCAAAAATATAAATTTAAATATTTA
66 TTTAAAAATTAAAATTTATATATCATCAAACACTTTTAGCCCAAAAATATAAATATAAATACTTA
* * * * * **
4935785 TTTTTCACTAAAATTAGATTGTTGTTTACTTAATTAATTTGTTACGTTAACTCTTACATGTTTAC
131 TTTTTCACTAAAATTAAACTGTTGTTTACTTAATTAACTTATTACATTAACTCTTACACATTTAC
* * *
4935850 ATTAAGATTTAAAATTTAGTTATTCCAACTTTATAAGTTTTTTTGTCAATTTTTACAG
196 ATTAAGATTTAAAATTTAATTAATCCAACGTTATAAGTTTTTTTGTCAATTTTTACAG
*
4935908 TTTTACGTCAAAATTTAGCTATGTCAATTTTAAATCATAATTATTTTTA-CGCTTATTATT-TTT
1 TTTTACGTCAAAATTTAGCTATGTCAATTTTAAATCATAATTATTTTAATC-CTTATTATTCTTT
* * * * * *
4935971 ATTTAAAAATTAAAA-TTATTATATTATTACATACTTTTAGCCCGATAATAT-AATATAAATACT
65 ATTTAAAAATTAAAATTTA-TATATCATCAAACACTTTTAGCCCAAAAATATAAATATAAATACT
* * *
4936034 TATTTTTTATTAAAATTAAACT-TT-TTTACTTAATTAACTTATTATATTAACTCTTACACATTT
129 TATTTTTCACTAAAATTAAACTGTTGTTTACTTAATTAACTTATTACATTAACTCTTACACATTT
** * *
4936097 ATGTTAAGATTTAAAATTTAATTAATCTACCGTTATAAGT
194 ACATTAAGATTTAAAATTTAATTAATCCAACGTTATAAGT
4936137 ATTTACGTCA
Statistics
Matches: 194, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
249 66 0.34
250 2 0.01
251 31 0.16
252 43 0.22
253 52 0.27
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (253 bp):
TTTTACGTCAAAATTTAGCTATGTCAATTTTAAATCATAATTATTTTAATCCTTATTATTCTTTA
TTTAAAAATTAAAATTTATATATCATCAAACACTTTTAGCCCAAAAATATAAATATAAATACTTA
TTTTTCACTAAAATTAAACTGTTGTTTACTTAATTAACTTATTACATTAACTCTTACACATTTAC
ATTAAGATTTAAAATTTAATTAATCCAACGTTATAAGTTTTTTTGTCAATTTTTACAG
Found at i:4936346 original size:20 final size:19
Alignment explanation
Indices: 4936323--4936368 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
4936313 AATTAATTTA
4936323 TTACGTTAA-ATTTTAAATAT
1 TTACGTTAAGA-TTTAAA-AT
4936343 TTACGTTAAGATTTAAAAT
1 TTACGTTAAGATTTAAAAT
4936362 TTA-GTTA
1 TTACGTTA
4936369 TTTCACCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.16
19 5 0.20
20 15 0.60
21 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (19 bp):
TTACGTTAAGATTTAAAAT
Found at i:4936539 original size:21 final size:21
Alignment explanation
Indices: 4936513--4936556 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4936503 GACTGAAATA
*
4936513 TAAATTTAAATATTTTTTA-T
1 TAAAATTAAATATTTTTTACT
* *
4936533 TAAAATTAGATTTTTTTTACT
1 TAAAATTAAATATTTTTTACT
4936554 TAA
1 TAA
4936557 TTGACTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TAAAATTAAATATTTTTTACT
Found at i:4937140 original size:252 final size:242
Alignment explanation
Indices: 4936678--4937155 Score: 496
Period size: 252 Copynumber: 1.9 Consensus size: 242
4936668 TTGAAATTTG
* * * * *
4936678 TATAATGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTTTTTTCACTAAAGTTAGAT
1 TATAATGTTAAACACTTTTAATTCGAGAATATAAATATAAATATTATTTTTCACTAAAATTAGAA
* * *
4936743 TTTTTTTACTTAATTGATTTGTTACGTTAACTTTCACATATTTATGTTAAGATTTAAAATTTAGT
66 ATTTTTTACTTAATTGACTTGTTACGTTAACTTTCACATATTTACGTTAAGATTTAAAATTTAGT
* * *
4936808 TATTCCACTTTTATAAATTTTTACATCAATTCTCATAGTTTAATGTCAAGGCTTTTCTATGTCAA
131 TATTCCACTTTTATAAATTTTTACATCAATTCTCACAGTTTAACGTCAAGGCTTTTCTATATCAA
* *
4936873 TTTTTGAATTATAATTATTTTTATCTTTATTATTATTTATTTAAAANNNNNNNNNNA
196 TTTGTGAACTATAATTATTTTTATCTTTATTATTATTTATTTAAAA----------A
* * *
4936930 TATATTGTTAAATACTTTTAA-TCTGAGAATATAAATATAAATGCTTATTTTTCACTAAAATTA-
1 TATAATGTTAAACACTTTTAATTC-GAGAATATAAATATAAAT-ATTATTTTTCACTAAAATTAG
* *
4936993 AAATTTTTTACTTAATTGACTTGTTATGTTAACTTTCGCATATTTACGTTAAGATTTAAAATTTA
64 AAATTTTTTACTTAATTGACTTGTTACGTTAACTTTCACATATTTACGTTAAGATTTAAAATTTA
********** * * * * *
4937058 GTTANNNNNNNNNNATAAGTTTTTACGTCAATTGTTACAGTTCT-ACGTCAAGGCTTTTTGTATA
129 GTTATTCCACTTTTATAAATTTTTACATCAATTCTCACAGTT-TAACGTCAAGGC-TTTTCTATA
*
4937122 TCAA-TTGTGAACTATAATTATTTTTATTTTTATT
192 TCAATTTGTGAACTATAATTATTTTTATCTTTATT
4937156 TAAAAAATAA
Statistics
Matches: 188, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
251 2 0.01
252 157 0.84
253 29 0.15
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.47
Consensus pattern (242 bp):
TATAATGTTAAACACTTTTAATTCGAGAATATAAATATAAATATTATTTTTCACTAAAATTAGAA
ATTTTTTACTTAATTGACTTGTTACGTTAACTTTCACATATTTACGTTAAGATTTAAAATTTAGT
TATTCCACTTTTATAAATTTTTACATCAATTCTCACAGTTTAACGTCAAGGCTTTTCTATATCAA
TTTGTGAACTATAATTATTTTTATCTTTATTATTATTTATTTAAAAA
Found at i:4948807 original size:2 final size:2
Alignment explanation
Indices: 4948800--4948825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4948790 ATAAAATGTA
4948800 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
4948826 GGTTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4956541 original size:16 final size:16
Alignment explanation
Indices: 4956510--4956540 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4956500 GATCCATTGA
4956510 CCCAAAAAAATTTTTT
1 CCCAAAAAAATTTTTT
4956526 CCC-AAAAAATTTTTT
1 CCCAAAAAAATTTTTT
4956541 TGCACCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.80
16 3 0.20
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (16 bp):
CCCAAAAAAATTTTTT
Found at i:4959771 original size:23 final size:23
Alignment explanation
Indices: 4959743--4959794 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
4959733 CACAAAGGCA
4959743 AAAACAAAACTTAAAAGTTGCCT
1 AAAACAAAACTTAAAAGTTGCCT
4959766 AAAACAAAACTTAAAAGTTGCCT
1 AAAACAAAACTTAAAAGTTGCCT
*
4959789 GAAACA
1 AAAACA
4959795 GGAAAATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (23 bp):
AAAACAAAACTTAAAAGTTGCCT
Found at i:4964303 original size:19 final size:19
Alignment explanation
Indices: 4964267--4964305 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4964257 CAAACAAAAA
*
4964267 TTTTAAAAATAAATAATTT
1 TTTTAAAAATAAAAAATTT
4964286 TTTTAAAAA-AATAAAATTT
1 TTTTAAAAATAA-AAAATTT
4964305 T
1 T
4964306 AAATAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAAAATAAAAAATTT
Found at i:4964305 original size:17 final size:18
Alignment explanation
Indices: 4964263--4964308 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
4964253 AAATCAAACA
4964263 AAAATTTTAAAAATAAAT
1 AAAATTTTAAAAATAAAT
** *
4964281 AATTTTTTTAAAA-AAAT
1 AAAATTTTAAAAATAAAT
4964298 AAAATTTTAAA
1 AAAATTTTAAA
4964309 TAAAGAGCTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTTTAAAAATAAAT
Found at i:4965603 original size:28 final size:28
Alignment explanation
Indices: 4965572--4965760 Score: 195
Period size: 27 Copynumber: 6.9 Consensus size: 28
4965562 CATTAGGGCA
* *
4965572 TGTAACAACTATAGTTTTCAACATAACG
1 TGTAACAACTACAATTTTCAACATAACG
* **
4965600 TGTAACAACTAC-ATTTTTAACATAAAA
1 TGTAACAACTACAATTTTCAACATAACG
* * *
4965627 TGTAACAACTACACTTTTCAACATAGCA
1 TGTAACAACTACAATTTTCAACATAACG
* *
4965655 TGTAACAACTA-AACTTTCAACATGACG
1 TGTAACAACTACAATTTTCAACATAACG
* * * *
4965682 TATAACAACTATATTTTTCAACATAGCG
1 TGTAACAACTACAATTTTCAACATAACG
* *
4965710 CGTAACAACTA-AATTTTTAACATAACG
1 TGTAACAACTACAATTTTCAACATAACG
* *
4965737 TATAACAACTACATTTTTCAACAT
1 TGTAACAACTACAATTTTCAACAT
4965761 GATGTATAAT
Statistics
Matches: 130, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
27 66 0.51
28 64 0.49
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (28 bp):
TGTAACAACTACAATTTTCAACATAACG
Found at i:4965637 original size:55 final size:55
Alignment explanation
Indices: 4965574--4965760 Score: 239
Period size: 55 Copynumber: 3.4 Consensus size: 55
4965564 TTAGGGCATG
* * * * * *
4965574 TAACAACTATAGTTTTCAACATAACGTGTAACAACTACATTTTTAACATAAAATG
1 TAACAACTACATTTTTCAACATAGCGTGTAACAACTAAATTTTTAACATAACATA
* * * * * *
4965629 TAACAACTACACTTTTCAACATAGCATGTAACAACTAAACTTTCAACATGACGTA
1 TAACAACTACATTTTTCAACATAGCGTGTAACAACTAAATTTTTAACATAACATA
* * *
4965684 TAACAACTATATTTTTCAACATAGCGCGTAACAACTAAATTTTTAACATAACGTA
1 TAACAACTACATTTTTCAACATAGCGTGTAACAACTAAATTTTTAACATAACATA
4965739 TAACAACTACATTTTTCAACAT
1 TAACAACTACATTTTTCAACAT
4965761 GATGTATAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 113 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (55 bp):
TAACAACTACATTTTTCAACATAGCGTGTAACAACTAAATTTTTAACATAACATA
Found at i:4965767 original size:28 final size:28
Alignment explanation
Indices: 4965574--4965769 Score: 191
Period size: 28 Copynumber: 7.1 Consensus size: 28
4965564 TTAGGGCATG
* * *
4965574 TAACAACTATAGTTTTCAACATAACGTG
1 TAACAACTACATTTTTCAACATAACGTA
** *
4965602 TAACAACTACATTTTT-AACATAAAATG
1 TAACAACTACATTTTTCAACATAACGTA
* * * *
4965629 TAACAACTACACTTTTCAACATAGCATG
1 TAACAACTACATTTTTCAACATAACGTA
** *
4965657 TAACAACTA-AACTTTCAACATGACGTA
1 TAACAACTACATTTTTCAACATAACGTA
* * **
4965684 TAACAACTATATTTTTCAACATAGCGCG
1 TAACAACTACATTTTTCAACATAACGTA
*
4965712 TAACAACTAAATTTTT-AACATAACGTA
1 TAACAACTACATTTTTCAACATAACGTA
* *
4965739 TAACAACTACATTTTTCAACATGATGTA
1 TAACAACTACATTTTTCAACATAACGTA
4965767 TAA
1 TAA
4965770 TTTTCAATAT
Statistics
Matches: 139, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 68 0.49
28 71 0.51
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (28 bp):
TAACAACTACATTTTTCAACATAACGTA
Found at i:4966316 original size:28 final size:28
Alignment explanation
Indices: 4966285--4966364 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
4966275 TATCATGGCA
4966285 TGTAACAACTACATTTTTCAACAT-AATG
1 TGTAACAACTACATTTTTCAACATGAA-G
*
4966313 TGTAACAACTA-AATTTTCAACATGAAG
1 TGTAACAACTACATTTTTCAACATGAAG
4966340 TGTAACAACTACATTTTTCAACATG
1 TGTAACAACTACATTTTTCAACATG
4966365 GTTTGTAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.48
28 25 0.52
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (28 bp):
TGTAACAACTACATTTTTCAACATGAAG
Found at i:4966345 original size:55 final size:55
Alignment explanation
Indices: 4966285--4966445 Score: 182
Period size: 55 Copynumber: 2.9 Consensus size: 55
4966275 TATCATGGCA
*
4966285 TGTAACAACTACATTTTTCAACATAATGTGTAACAACTAAATTTTCAACATGAAG
1 TGTAACAACTACATTTTTCAACATAGTGTGTAACAACTAAATTTTCAACATGAAG
* * * * **
4966340 TGTAACAACTACATTTTTCAACATGGTTTGTAATAACTAAACTTTCAACATGGCG
1 TGTAACAACTACATTTTTCAACATAGTGTGTAACAACTAAATTTTCAACATGAAG
** * * * *
4966395 CATAACAACTA-ATTTTTTAAAATAGTGTATAACAAC-AACATTTTTAACATG
1 TGTAACAACTACATTTTTCAACATAGTGTGTAACAACTAA-ATTTTCAACATG
4966446 GTGTGCAATA
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
53 2 0.02
54 29 0.33
55 57 0.65
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (55 bp):
TGTAACAACTACATTTTTCAACATAGTGTGTAACAACTAAATTTTCAACATGAAG
Found at i:4966392 original size:27 final size:27
Alignment explanation
Indices: 4966285--4966465 Score: 123
Period size: 27 Copynumber: 6.6 Consensus size: 27
4966275 TATCATGGCA
* *
4966285 TGTAACAACTACATTTTTCAACAT-AATG
1 TGTAACAACTA-AATTTTCAACATGGA-G
*
4966313 TGTAACAACTAAATTTTCAACATGAAG
1 TGTAACAACTAAATTTTCAACATGGAG
* **
4966340 TGTAACAACTACATTTTTCAACATGGTT
1 TGTAACAACTA-AATTTTCAACATGGAG
* * *
4966368 TGTAATAACTAAACTTTCAACATGGCG
1 TGTAACAACTAAATTTTCAACATGGAG
** * * * * *
4966395 CATAACAACTAATTTTTTAAAATAGTG
1 TGTAACAACTAAATTTTCAACATGGAG
* * *
4966422 TATAACAAC-AACATTTTTAACATGGTG
1 TGTAACAACTAA-ATTTTCAACATGGAG
* *
4966449 TGCAATAACTAAATTTT
1 TGTAACAACTAAATTTT
4966466 AGAACATGAC
Statistics
Matches: 123, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 84 0.68
28 37 0.30
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (27 bp):
TGTAACAACTAAATTTTCAACATGGAG
Found at i:4966481 original size:109 final size:110
Alignment explanation
Indices: 4966287--4966502 Score: 240
Period size: 109 Copynumber: 2.0 Consensus size: 110
4966277 TCATGGCATG
* * * *
4966287 TAACAACTACATTTTTCAACATAATGTGTAACAACTAAATTTTCAACATGAAGTGTAACAACTAC
1 TAACAACTACATTTTTCAAAATAATGTATAACAACTAAATTTTCAACATGAAGTGCAACAACTAA
* ***
4966352 ATTTTTCAACATGGTTTGTAATAACTA-AACTTTCAACATGGCGCA
66 ATTTTACAACATGACATGTAAT-ACTATAACTTTCAACATGGCGCA
* * * ** *
4966397 TAACAACTA-ATTTTTTAAAATAGTGTATAACAAC-AACATTTTTAACATGGTGTGCAATAACTA
1 TAACAACTACATTTTTCAAAATAATGTATAACAACTAA-ATTTTCAACATGAAGTGCAACAACTA
* **
4966460 AATTTTAGAACATGACATGTAATACTATATTTTTCAACATGGC
65 AATTTTACAACATGACATGTAATACTATAACTTTCAACATGGC
4966503 ATTAACAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
108 6 0.07
109 72 0.83
110 9 0.10
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (110 bp):
TAACAACTACATTTTTCAAAATAATGTATAACAACTAAATTTTCAACATGAAGTGCAACAACTAA
ATTTTACAACATGACATGTAATACTATAACTTTCAACATGGCGCA
Found at i:4966954 original size:28 final size:28
Alignment explanation
Indices: 4966923--4967149 Score: 155
Period size: 27 Copynumber: 8.3 Consensus size: 28
4966913 TTATCATGGC
*
4966923 GTGTAACAACTGCATTTTTCAACAT-AA
1 GTGTAACAACTACATTTTTCAACATGAA
* *
4966950 TGTGTAACAATTAAATTTTT-AACATGAA
1 -GTGTAACAACTACATTTTTCAACATGAA
**
4966978 GTGTAACAACTACATTTTTCAACATGGT
1 GTGTAACAACTACATTTTTCAACATGAA
* * * * **
4967006 TTGTAATAACTA-AATCTTCAACATGTT
1 GTGTAACAACTACATTTTTCAACATGAA
** * *
4967033 GCATAACAACTAAATTTTT-AACATGAT
1 GTGTAACAACTACATTTTTCAACATGAA
* * *
4967060 GTATGACAACTACATTTTT-AACATGGTA
1 GTGTAACAACTACATTTTTCAACAT-GAA
* * ** *
4967088 -TGTAATAACTAAATTTTAGAACATGAC
1 GTGTAACAACTACATTTTTCAACATGAA
* *
4967115 GTGTAA-TACTACATTTTTCAACATGAC
1 GTGTAACAACTACATTTTTCAACATGAA
4967142 GT-TAACAA
1 GTGTAACAA
4967150 TATTTTTTCC
Statistics
Matches: 156, Mismatches: 36, Indels: 15
0.75 0.17 0.07
Matches are distributed among these distances:
26 3 0.02
27 104 0.67
28 49 0.31
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (28 bp):
GTGTAACAACTACATTTTTCAACATGAA
Found at i:4967011 original size:55 final size:55
Alignment explanation
Indices: 4966923--4967149 Score: 183
Period size: 55 Copynumber: 4.2 Consensus size: 55
4966913 TTATCATGGC
* * *
4966923 GTGTAACAACTGCATTTTTCAACATAATGTGTAACAATTAAATTTTTAACATGAA
1 GTGTAACAACTACATTTTTCAACATGATGTGTAACAACTAAATTTTTAACATGAA
* * * * * **
4966978 GTGTAACAACTACATTTTTCAACATGGTTTGTAATAACTAAATCTTCAACATGTT
1 GTGTAACAACTACATTTTTCAACATGATGTGTAACAACTAAATTTTTAACATGAA
** * * * * *
4967033 GCATAACAACTAAATTTTT-AACATGATGTATGACAACTACATTTTTAACATGGTA
1 GTGTAACAACTACATTTTTCAACATGATGTGTAACAACTAAATTTTTAACAT-GAA
* * ** * * * *
4967088 -TGTAATAACTAAATTTTAGAACATGACGTGTAA-TACTACATTTTTCAACATGAC
1 GTGTAACAACTACATTTTTCAACATGATGTGTAACAACTAAATTTTT-AACATGAA
4967142 GT-TAACAA
1 GTGTAACAA
4967150 TATTTTTTCC
Statistics
Matches: 135, Mismatches: 33, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
54 55 0.41
55 80 0.59
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (55 bp):
GTGTAACAACTACATTTTTCAACATGATGTGTAACAACTAAATTTTTAACATGAA
Found at i:4967138 original size:82 final size:82
Alignment explanation
Indices: 4966954--4967149 Score: 227
Period size: 82 Copynumber: 2.4 Consensus size: 82
4966944 ACATAATGTG
* * *
4966954 TAACAATTAAATTTTTAACATGAAGTGTAACAACTACATTTTTCAACATGGTTTGTAATAACTAA
1 TAACAACTAAATTTTTAACATGAAGTATAACAACTACATTTTTCAACATGGTATGTAATAACTAA
**
4967019 ATCTTCAACATGTTGCA
66 ATCTTCAACATGACGCA
* *
4967036 TAACAACTAAATTTTTAACATGATGTATGACAACTACATTTTT-AACATGGTATGTAATAACTAA
1 TAACAACTAAATTTTTAACATGAAGTATAACAACTACATTTTTCAACATGGTATGTAATAACTAA
* * **
4967100 ATTTTAGAACATGACGTG
66 ATCTT-CAACATGACGCA
* * *
4967118 TAA-TACTACATTTTTCAACATGACGT-TAACAA
1 TAACAACTAAATTTTT-AACATGAAGTATAACAA
4967150 TATTTTTTCC
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
81 39 0.40
82 58 0.60
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (82 bp):
TAACAACTAAATTTTTAACATGAAGTATAACAACTACATTTTTCAACATGGTATGTAATAACTAA
ATCTTCAACATGACGCA
Found at i:4967158 original size:638 final size:637
Alignment explanation
Indices: 4965781--4967190 Score: 2216
Period size: 638 Copynumber: 2.2 Consensus size: 637
4965771 TTTCAATATG
* * * * * * *
4965781 GTGTGTAACAACTATATGTTTAACATAGCATGTAACAACTAAATTTTAGAACATGACGTATAATA
1 GTGTATAACAACTACATTTTTAACATGGTATGTAATAACTAAATTTTAGAACATGACGTGTAATA
*
4965846 CTACATTTTTCAACATGGCGTTAACAATATTTTTCCCACAAAAAGTAACAATAACATTTCCC-GA
66 CTACATTTTTCAACATGGCGTTAACAATATTTTT-TCACAAAAAGTAACAATAACATTTCCCAG-
*
4965910 CATGCCTCTAACATGGCAAGTGAATTGAATTTTTGGTGACGATGTCATTTTGTCTAGGGAAAAAA
129 CATGCCTCTAACATGGCAAGTGAATTGAATTTTTGGTGACGATGCCATTTTGTCTAGGGAAAAAA
* *
4965975 AACTTTATTTTCCCTTATTTGATTACTTTGATTGGTTAAAATTTTCCATCATATTAGTTTTCCCA
194 AACTTTATTTTCCCTTATTTGATTACTTTCATTAGTTAAAATTTTCCATCATATTAGTTTTCCCA
* *
4966040 CCATCAACCCAAATTACCCACATTCTACCTCCTATTCTCTCATTTCCAATCCACGTCTCCTCTCT
259 CCATCAACCCAAATTACCCACATTCTACCTCCTATTCTCTCATCTCCAATCCACATCTCCTCTCT
* * * *
4966105 AATCATTTTCCCTTTCCATCGTCTCACAATCTAGTTAGGTATCTGTTGCTATCAACTTATTAGAT
324 AATCATTTTCACTTTCCATCGTCTCACAATCTAGTCAGGTATCCGTTGCTATCAACTTATCAGAT
4966170 ATTGTCTGTCTTATCATATAAGGTACGAAAAGGTAAGTTTAATAAAAAGTCTTTTCTATCATGTC
389 ATTGTCTGTCTTATCATATAAGGTACGAAAAGGTAAGTTTAATAAAAAGTCTTTTCTATCATGTC
* *
4966235 AAAATAGTTCAAATTAGGATAAGACGTGTAATAATTTTTTTATCATGGCATGTAACAACTACATT
454 AAAACAGTTCAAATTAGGATAAGACATGTAATAATTTTTTTATCATGGCATGTAACAACTACATT
4966300 TTTCAACATAATGTGTAACAACTAAATTTTCAACATGAAGTGTAACAACTACATTTTTCAACATG
519 TTTCAACATAATGTGTAACAACTAAATTTTCAACATGAAGTGTAACAACTACATTTTTCAACATG
*
4966365 GTTTGTAATAACTAAACTTTCAACATGGCGCATAACAACTAATTTTTTAAAATA
584 GTTTGTAATAACTAAACTTTCAACATGGCGCATAACAACTAAATTTTTAAAATA
* * * *
4966419 GTGTATAACAACAACATTTTTAACATGGTGTGCAATAACTAAATTTTAGAACATGACATGTAATA
1 GTGTATAACAACTACATTTTTAACATGGTATGTAATAACTAAATTTTAGAACATGACGTGTAATA
* * *
4966484 CTATATTTTTCAACATGGCATTAACAATATTTTTTTCTCAAAAAGTAACAATAACATTTCCCAGC
66 CTACATTTTTCAACATGGCGTTAACAATA-TTTTTTCACAAAAAGTAACAATAACATTTCCCAGC
** *
4966549 ATGCCTCTAATGTGGCAAGTGAATTGGATTTTTGGTGACGATGCCATTTTGTCTA-GGAAAAAAT
130 ATGCCTCTAACATGGCAAGTGAATTGAATTTTTGGTGACGATGCCATTTTGTCTAGGGAAAAAA-
* * *
4966613 AACTTTATTTTTCCTTATTTGATTACTTTCATTAGTTAAAATTTTCCATCATTTTAGTTTTTCCA
194 AACTTTATTTTCCCTTATTTGATTACTTTCATTAGTTAAAATTTTCCATCATATTAGTTTTCCCA
* * *
4966678 CCATCAACCCAAATTACCCACATTCTACCTCTTCTTCTCTCATCTCCAATCTACATCTCCTCTCT
259 CCATCAACCCAAATTACCCACATTCTACCTCCTATTCTCTCATCTCCAATCCACATCTCCTCTCT
* *
4966743 AATCATTTTCAGTTTCCATCGTCTCACCATCTAGTCAGGTATCCGTTGCTATCAACTTATCAGAT
324 AATCATTTTCACTTTCCATCGTCTCACAATCTAGTCAGGTATCCGTTGCTATCAACTTATCAGAT
* * * * * *
4966808 ATTGTCTGTCTTGTCGTGTAAGGTACGAAAAGGTAGGTTTATTAAAAAGTTTTTTCTATCATGTC
389 ATTGTCTGTCTTATCATATAAGGTACGAAAAGGTAAGTTTAATAAAAAGTCTTTTCTATCATGTC
* * *
4966873 AAAACAGTTCAAATTAGGATAAGGCATGTAATAATTTTTTTTATCATGGCGTGTAACAACTGCAT
454 AAAACAGTTCAAATTAGGATAAGACATGTAATAA-TTTTTTTATCATGGCATGTAACAACTACAT
* *
4966938 TTTTCAACATAATGTGTAACAATTAAATTTTTAACATGAAGTGTAACAACTACATTTTTCAACAT
518 TTTTCAACATAATGTGTAACAACTAAATTTTCAACATGAAGTGTAACAACTACATTTTTCAACAT
** *
4967003 GGTTTGTAATAACTAAA-TCTTCAACATGTTGCATAACAACTAAATTTTTAACAT-
583 GGTTTGTAATAACTAAACT-TTCAACATGGCGCATAACAACTAAATTTTTAAAATA
*
4967057 GATGTATGACAACTACATTTTTAACATGGTATGTAATAACTAAATTTTAGAACATGACGTGTAAT
1 G-TGTATAACAACTACATTTTTAACATGGTATGTAATAACTAAATTTTAGAACATGACGTGTAAT
* * *
4967122 ACTACATTTTTCAACATGACGTTAACAATATTTTTTCCACAAAAAGTAACAATAACATCTCCCAA
65 ACTACATTTTTCAACATGGCGTTAACAATATTTTTT-CACAAAAAGTAACAATAACATTTCCCAG
4967187 CATG
129 CATG
4967191 TTATATAACA
Statistics
Matches: 702, Mismatches: 63, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
637 8 0.01
638 435 0.62
639 259 0.37
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.37
Consensus pattern (637 bp):
GTGTATAACAACTACATTTTTAACATGGTATGTAATAACTAAATTTTAGAACATGACGTGTAATA
CTACATTTTTCAACATGGCGTTAACAATATTTTTTCACAAAAAGTAACAATAACATTTCCCAGCA
TGCCTCTAACATGGCAAGTGAATTGAATTTTTGGTGACGATGCCATTTTGTCTAGGGAAAAAAAA
CTTTATTTTCCCTTATTTGATTACTTTCATTAGTTAAAATTTTCCATCATATTAGTTTTCCCACC
ATCAACCCAAATTACCCACATTCTACCTCCTATTCTCTCATCTCCAATCCACATCTCCTCTCTAA
TCATTTTCACTTTCCATCGTCTCACAATCTAGTCAGGTATCCGTTGCTATCAACTTATCAGATAT
TGTCTGTCTTATCATATAAGGTACGAAAAGGTAAGTTTAATAAAAAGTCTTTTCTATCATGTCAA
AACAGTTCAAATTAGGATAAGACATGTAATAATTTTTTTATCATGGCATGTAACAACTACATTTT
TCAACATAATGTGTAACAACTAAATTTTCAACATGAAGTGTAACAACTACATTTTTCAACATGGT
TTGTAATAACTAAACTTTCAACATGGCGCATAACAACTAAATTTTTAAAATA
Found at i:4967398 original size:23 final size:23
Alignment explanation
Indices: 4967368--4967412 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4967358 CTTGGTATAT
*
4967368 CAACACTTCGTACAAACCATTAG
1 CAACACTTCATACAAACCATTAG
*
4967391 CAACACTTCATACAAATCATTA
1 CAACACTTCATACAAACCATTA
4967413 ATAAATTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.24
Consensus pattern (23 bp):
CAACACTTCATACAAACCATTAG
Found at i:4972775 original size:212 final size:205
Alignment explanation
Indices: 4972372--4972787 Score: 493
Period size: 212 Copynumber: 2.0 Consensus size: 205
4972362 AACAAAAATT
* * * *
4972372 ATATATATAGGTATACACATTATATATAATGAAAATTTGAAAATTTTCAAAACGACATAATAATG
1 ATATATATAGGTATACACATAATATATAAGGAAAATTTGAAAA-TTTCAAAACAAAATAATAATG
* * * *
4972437 ATAAATTTGATGTACTGTATATGAAAAATTTTTATTGATGTACAACAACAAAAATTATAAATTAA
65 ATAAATTTGATCTACTATATATGAAAAATGTTTATTGATGTACAAAAACAAAAATTATAAATTAA
* * * *
4972502 ATATATATAATAGGATATATATAATGATAAATTTGATGCACTATTTATGAATAATTTATAATGAT
130 ATATATATAATA-GATATATATAATAATAAATTTGAGGCACAATGTATGAATAATTTATAATGAT
*
4972567 TTACAATAACAA
194 TTAAAATAACAA
*
4972579 ATATATATAGGTATATACATAATATATAAGGAAAATTTGAAAA-TT-AAAA-AAAATTAATAATG
1 ATATATATAGGTATACACATAATATATAAGGAAAATTTGAAAATTTCAAAACAAAA-TAATAATG
*
4972641 ATAAATTTGATCTACTATATAT-ACAAAATGTTTATTGATGTACGAAAAAAATAAAAATCAAATA
65 ATAAATTTGATCTACTATATATGA-AAAATGTTTATTGATGTAC---AAAAACAAAAAT----TA
* * *
4972705 TATATGTAATAGTATATATAATA-ATA-ATAATAATAATAAATTTGAGGTACAATGTATGCATAA
122 TAAAT-TAA-A-TATATATAATAGATATAT-ATAATAATAAATTTGAGGCACAATGTATGAATAA
4972768 TTTATAATGATTTAAAATAA
183 TTTATAATGATTTAAAATAA
4972788 TAAAAATTAT
Statistics
Matches: 178, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
203 3 0.02
204 50 0.28
205 2 0.01
207 50 0.28
211 8 0.04
212 53 0.30
213 1 0.01
214 11 0.06
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (205 bp):
ATATATATAGGTATACACATAATATATAAGGAAAATTTGAAAATTTCAAAACAAAATAATAATGA
TAAATTTGATCTACTATATATGAAAAATGTTTATTGATGTACAAAAACAAAAATTATAAATTAAA
TATATATAATAGATATATATAATAATAAATTTGAGGCACAATGTATGAATAATTTATAATGATTT
AAAATAACAA
Found at i:4973075 original size:72 final size:73
Alignment explanation
Indices: 4972929--4973067 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 73
4972919 GACGTACTAT
* * * * *
4972929 ATATGCATAATTTTTAATGATTTAGGAGAACATGTATTATATATATAGGGTTATAAATTATATAT
1 ATATGCATAATTTTTAATGAGTTAGAAGAACATGGATTATACATATAAGGTTATAAATTATATAT
4972994 AACAATAA
66 AACAATAA
*
4973002 ATATGCAT-ATTTTTAATGAGTTAGAAGAGCATGGATTATACATATAAGGTTATAAATTATATAT
1 ATATGCATAATTTTTAATGAGTTAGAAGAACATGGATTATACATATAAGGTTATAAATTATATAT
4973066 AA
66 AA
4973068 TGATAAATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 52 0.87
73 8 0.13
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (73 bp):
ATATGCATAATTTTTAATGAGTTAGAAGAACATGGATTATACATATAAGGTTATAAATTATATAT
AACAATAA
Found at i:4975163 original size:18 final size:17
Alignment explanation
Indices: 4975136--4975195 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
4975126 ATTGACTAGA
*
4975136 AGGTTTAATAGATTTTT
1 AGGTTCAATAGATTTTT
4975153 ATGGTTCAATAGA-----
1 A-GGTTCAATAGATTTTT
4975166 AGGTTCAATAGATTTTT
1 AGGTTCAATAGATTTTT
4975183 AAGGTTCAATAGA
1 -AGGTTCAATAGA
4975196 AGTAGAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
12 11 0.31
13 1 0.03
17 1 0.03
18 22 0.63
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (17 bp):
AGGTTCAATAGATTTTT
Found at i:4975168 original size:30 final size:30
Alignment explanation
Indices: 4975132--4975197 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
4975122 CACTATTGAC
* *
4975132 TAGAAGGTTTAATAGATTTTTATGGTTCAA
1 TAGAAGGTTCAATAGATTTTTAAGGTTCAA
4975162 TAGAAGGTTCAATAGATTTTTAAGGTTCAA
1 TAGAAGGTTCAATAGATTTTTAAGGTTCAA
4975192 TAGAAG
1 TAGAAG
4975198 TAGAAAACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (30 bp):
TAGAAGGTTCAATAGATTTTTAAGGTTCAA
Found at i:4984082 original size:29 final size:29
Alignment explanation
Indices: 4984032--4984122 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
4984022 TTAGTGTGGA
*
4984032 TTTGTGGTGTGTCC-GTTAAAAACCATGGG
1 TTTGTGGTGAG-CCTGTTAAAAACCATGGG
* *
4984061 TTTGTGGTGAGCCTGTTGAAAACCATGGA
1 TTTGTGGTGAGCCTGTTAAAAACCATGGG
* * *
4984090 TTTGTGGTTGAACTTGTTAAAAAGCATGGG
1 TTTGTGG-TGAGCCTGTTAAAAACCATGGG
4984120 TTT
1 TTT
4984123 CACTTTATCT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
28 2 0.04
29 30 0.58
30 20 0.38
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (29 bp):
TTTGTGGTGAGCCTGTTAAAAACCATGGG
Found at i:4984849 original size:7 final size:8
Alignment explanation
Indices: 4984824--4984861 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
4984814 GTCACCATCG
*
4984824 TTTCTCTT
1 TTTCACTT
4984832 TTTCACTT
1 TTTCACTT
4984840 TTTCACTT
1 TTTCACTT
*
4984848 TTTCATTT
1 TTTCACTT
4984856 TTTCAC
1 TTTCAC
4984862 CTATCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTCACTT
Found at i:4994828 original size:3 final size:3
Alignment explanation
Indices: 4994820--4994882 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
4994810 CATAATTGAA
4994820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4994868 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
4994883 GTCGAACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4995722 original size:78 final size:79
Alignment explanation
Indices: 4995568--4995722 Score: 183
Period size: 78 Copynumber: 2.0 Consensus size: 79
4995558 TTCCACAATA
* * *
4995568 AAAGAAAGTCAAATCTTTTTTTTCTCTTCCCTAGAATTTGTAAGAAAAAATTGATGCTCTTTACT
1 AAAGAAAGTCAAATC-TTTTCTCCTCTTCCCTAGAATCTGTAAGAAAAAATTGATGCTCTTTACT
*
4995633 TCCTTATAATCTGTG
65 TCCTTAAAATCTGTG
* * *
4995648 AAAGAAAGTCAAATC-TTTCTCCTCTTTCCTAGAATCTGTAA-AGAAACTTCGATGCT-TTT-CT
1 AAAGAAAGTCAAATCTTTTCTCCTCTTCCCTAGAATCTGTAAGAAAAAATT-GATGCTCTTTACT
4995709 CTCCTCTAAAATCT
65 -TCCT-TAAAATCT
4995723 AAGAGGAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 2 0.03
77 13 0.20
78 35 0.54
80 15 0.23
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (79 bp):
AAAGAAAGTCAAATCTTTTCTCCTCTTCCCTAGAATCTGTAAGAAAAAATTGATGCTCTTTACTT
CCTTAAAATCTGTG
Found at i:5009664 original size:18 final size:18
Alignment explanation
Indices: 5009641--5009675 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5009631 AGAATGTGAG
5009641 TCTTCTCTAATTATGGTA
1 TCTTCTCTAATTATGGTA
* *
5009659 TCTTCTTTAATTTTGGT
1 TCTTCTCTAATTATGGT
5009676 GATTGGGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.57
Consensus pattern (18 bp):
TCTTCTCTAATTATGGTA
Found at i:5012609 original size:18 final size:19
Alignment explanation
Indices: 5012574--5012608 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5012564 TTCCTTTAAT
5012574 TTTTCATCTTTTTCTTTTC
1 TTTTCATCTTTTTCTTTTC
5012593 TTTTC-TCTTTTT-TTTT
1 TTTTCATCTTTTTCTTTT
5012609 TAACTCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCATCTTTTTCTTTTC
Found at i:5014127 original size:32 final size:33
Alignment explanation
Indices: 5014091--5014176 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 33
5014081 NNNNNNNNNA
*
5014091 AAATTGTTTAATTAAGTT-GTGCCTAATTCATT
1 AAATTGTTTAATTAAGTTGGGGCCTAATTCATT
* *
5014123 AAATTGTTTAATTAAGTTATGGGGCGTAATTGATT
1 AAATTGTTTAATTAAG-T-TGGGGCCTAATTCATT
*
5014158 AAATTTGTTTAATCAAGTT
1 AAA-TTGTTTAATTAAGTT
5014177 ATTGAGCTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 16 0.35
33 1 0.02
34 2 0.04
35 15 0.33
36 12 0.26
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (33 bp):
AAATTGTTTAATTAAGTTGGGGCCTAATTCATT
Found at i:5014176 original size:36 final size:35
Alignment explanation
Indices: 5014114--5014202 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 35
5014104 AAGTTGTGCC
* * *
5014114 TAATTCATTAAATTGTTTAATTAAGTTATGGGGCG
1 TAATTGATTAAATTGTTTAATCAAGTTATGGAGCG
* *
5014149 TAATTGATTAAATTTGTTTAATCAAGTTATTGAGCT
1 TAATTGATTAAA-TTGTTTAATCAAGTTATGGAGCG
*
5014185 TAATTGATCAAATTGTTT
1 TAATTGATTAAATTGTTT
5014203 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 17 0.36
36 30 0.64
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.46
Consensus pattern (35 bp):
TAATTGATTAAATTGTTTAATCAAGTTATGGAGCG
Found at i:5019847 original size:10 final size:10
Alignment explanation
Indices: 5019832--5019861 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5019822 TCTCGAATTG
5019832 ATTCAAAGTA
1 ATTCAAAGTA
*
5019842 ATTCAAAATA
1 ATTCAAAGTA
5019852 ATTCAAAGTA
1 ATTCAAAGTA
5019862 GGGGTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (10 bp):
ATTCAAAGTA
Found at i:5028990 original size:14 final size:15
Alignment explanation
Indices: 5028971--5029001 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5028961 AAAAAAAGTT
5028971 AAAATCTTTTT-TTA
1 AAAATCTTTTTATTA
5028985 AAAATCTTTTTATTA
1 AAAATCTTTTTATTA
5029000 AA
1 AA
5029002 TGAGTATTTT
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:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAATCTTTTTATTA
Found at i:5030390 original size:20 final size:22
Alignment explanation
Indices: 5030351--5030403 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5030341 CTAAACTTAC
* *
5030351 AAAATTAATGTTTTACATTA-A
1 AAAAATAATATTTTACATTATA
5030372 AAAAATAATATTTTA-ATTATA
1 AAAAATAATATTTTACATTATA
*
5030393 AATAA-AATATT
1 AAAAATAATATT
5030404 AATATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAATAATATTTTACATTATA
Found at i:5030437 original size:15 final size:15
Alignment explanation
Indices: 5030396--5030430 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
5030386 AATTATAAAT
5030396 AAAATATTAATATTTTA
1 AAAATATT-A-ATTTTA
5030413 AAAATATTAATTTTA
1 AAAATATTAATTTTA
5030428 AAA
1 AAA
5030431 TTTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATATTAATTTTA
Found at i:5030809 original size:42 final size:41
Alignment explanation
Indices: 5030752--5030986 Score: 134
Period size: 42 Copynumber: 5.8 Consensus size: 41
5030742 ATAATTATAG
*
5030752 TTAATTTATAAATAAAATATTAATATTTTAAAATTTCAATGA
1 TTAAATTATAAATAAAATATTAATATTTTAAAATTTCAAT-A
* *
5030794 TTAAATTATAAATAAAATATTAACA-TTT-AAATGATCAAAATA
1 TTAAATTATAAATAAAATATTAATATTTTAAAAT-TTC--AATA
* * * * *
5030836 TTAATATTTTAAATAAATTA-TAAAATATTAATATTT-AA-A
1 TTAA-ATTATAAATAAAATATTAATATTTTAAAATTTCAATA
* * * * * *
5030875 ATAAAATA-AAATAAAA-ATAAATA-ATCATAA---CAATA
1 TTAAATTATAAATAAAATATTAATATTTTAAAATTTCAATA
* * *
5030910 TTTAAATTATAAATAATATATTAATGTTTTATAATATT-AATGA
1 -TTAAATTATAAATAAAATATTAATATTTTAAAAT-TTCAAT-A
* *
5030953 TTAAATTATAATTAAAATATTAATTTTTTTAAAA
1 TTAAATTATAAATAAAATATTAA-TATTTTAAAA
5030987 AATAAAAATA
Statistics
Matches: 145, Mismatches: 29, Indels: 37
0.69 0.14 0.18
Matches are distributed among these distances:
34 2 0.01
35 1 0.01
36 11 0.08
37 17 0.12
38 7 0.05
39 9 0.06
40 6 0.04
41 5 0.03
42 56 0.39
43 28 0.19
44 3 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (41 bp):
TTAAATTATAAATAAAATATTAATATTTTAAAATTTCAATA
Found at i:5030863 original size:27 final size:26
Alignment explanation
Indices: 5030805--5030887 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 26
5030795 TAAATTATAA
* *
5030805 ATAAAATATTAACATTT-AAAT-GAT
1 ATAAAATATTAATATTTAAAATAAAT
* *
5030829 -CAAAATATTAATATTTTAAATAAATT
1 ATAAAATATTAATATTTAAAATAAA-T
5030855 ATAAAATATTAATATTTAAAATAAA-
1 ATAAAATATTAATATTTAAAATAAAT
5030880 ATAAAATA
1 ATAAAATA
5030888 AAAATAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 14 0.28
24 4 0.08
25 9 0.18
26 1 0.02
27 22 0.44
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (26 bp):
ATAAAATATTAATATTTAAAATAAAT
Found at i:5030876 original size:15 final size:15
Alignment explanation
Indices: 5030830--5030877 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
5030820 TTAAATGATC
5030830 AAAATATTAATATTT
1 AAAATATTAATATTT
* *
5030845 TAAATA--AAT-TAT
1 AAAATATTAATATTT
5030857 AAAATATTAATATTT
1 AAAATATTAATATTT
5030872 AAAATA
1 AAAATA
5030878 AAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 3 0.12
15 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATATTAATATTT
Found at i:5030893 original size:25 final size:26
Alignment explanation
Indices: 5030838--5030893 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
5030828 TCAAAATATT
* **
5030838 AATATTTTAAATAAATTATAAAATATT
1 AATATTTAAAATAAA-TATAAAATAAA
5030865 AATATTTAAAATAAA-ATAAAATAAA
1 AATATTTAAAATAAATATAAAATAAA
5030890 AATA
1 AATA
5030894 AATAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.46
27 14 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AATATTTAAAATAAATATAAAATAAA
Found at i:5031573 original size:46 final size:46
Alignment explanation
Indices: 5031520--5031620 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
5031510 ATAATTTTTT
* *
5031520 TATAAATATGTGATTAAATTATAA-TAAGGCTAATTTAATCTTTTGG
1 TATAAATATGTGATTAAAGTATAATTAAGGAT-ATTTAATCTTTTGG
* * * *
5031566 TATAAATATTTTATTATAGTATAATTAAGGATATTTTATCTTTTGG
1 TATAAATATGTGATTAAAGTATAATTAAGGATATTTAATCTTTTGG
*
5031612 TATATATAT
1 TATAAATAT
5031621 TTTCATCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 41 0.87
47 6 0.13
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (46 bp):
TATAAATATGTGATTAAAGTATAATTAAGGATATTTAATCTTTTGG
Found at i:5041020 original size:80 final size:80
Alignment explanation
Indices: 5040922--5041211 Score: 368
Period size: 80 Copynumber: 3.6 Consensus size: 80
5040912 TATCATCATA
* * * * * * *
5040922 CTTAGCCCATAGTATATATGACTATCTCAGCACATACATTTCATGGCATATATTTCATAGTCTCG
1 CTTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAGCCTCA
*
5040987 TAAATCACTTGCATG
66 TAAATCACTTACATG
* * *
5041002 CTTCGCCCATAATGTATATGACCATCTCAACATATACATCTCATGGCATACATTTCATAGCCTCA
1 CTTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAGCCTCA
5041067 TAAATCACTTACATG
66 TAAATCACTTACATG
* * * **
5041082 CTTAGCCCATAGTGTATATAACTATTTCAACATTTACATCTCATGGCATACATTTCATAGCCTCA
1 CTTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAGCCTCA
*
5041147 TAAATCACTTACATA
66 TAAATCACTTACATG
* * *
5041162 CTTAGCCCA-AAGTTTACATGA-TATACTTAACACATACATCTCATGGCATA
1 CTTAGCCCATAA-TGTATATGACTAT-CTCAACACATACATCTCATGGCATA
5041212 TATGTTACAA
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
79 4 0.02
80 178 0.98
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (80 bp):
CTTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAGCCTCA
TAAATCACTTACATG
Found at i:5041159 original size:40 final size:40
Alignment explanation
Indices: 5041036--5041160 Score: 100
Period size: 40 Copynumber: 3.1 Consensus size: 40
5041026 TCTCAACATA
5041036 TACATCTCATGGCATACATTTCATAGCCTCATAAATCACT
1 TACATCTCATGGCATACATTTCATAGCCTCATAAATCACT
* * * * * *
5041076 TACATGCTTA-GCCCATA-GTGTAT-ATA-ACT-ATTTCAA-CATT
1 TACAT-CTCATG-GCATACAT-T-TCATAGCCTCA--TAAATCACT
5041116 TACATCTCATGGCATACATTTCATAGCCTCATAAATCACT
1 TACATCTCATGGCATACATTTCATAGCCTCATAAATCACT
5041156 TACAT
1 TACAT
5041161 ACTTAGCCCA
Statistics
Matches: 61, Mismatches: 12, Indels: 24
0.63 0.12 0.25
Matches are distributed among these distances:
38 1 0.02
39 15 0.25
40 29 0.48
41 15 0.25
42 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (40 bp):
TACATCTCATGGCATACATTTCATAGCCTCATAAATCACT
Found at i:5060942 original size:13 final size:13
Alignment explanation
Indices: 5060924--5060956 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5060914 GTATAATATA
5060924 AACAACAATTAAC
1 AACAACAATTAAC
*
5060937 AACAACAATTGAC
1 AACAACAATTAAC
5060950 AA-AACAA
1 AACAACAA
5060957 AAAGACACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (13 bp):
AACAACAATTAAC
Found at i:5066646 original size:2 final size:2
Alignment explanation
Indices: 5066639--5066665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5066629 TTCGACTGTG
5066639 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5066666 TAAATCAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5067266 original size:23 final size:23
Alignment explanation
Indices: 5067238--5067286 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5067228 TAAACACATT
5067238 AATTCAATGTAATAATTTAAA-AA
1 AATTCAATGTAA-AATTTAAATAA
*
5067261 AATTCAATTTAAAATTTAAATAA
1 AATTCAATGTAAAATTTAAATAA
5067284 AAT
1 AAT
5067287 AATTGATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AATTCAATGTAAAATTTAAATAA
Found at i:5068248 original size:15 final size:16
Alignment explanation
Indices: 5068218--5068259 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5068208 CTATTTTGTG
*
5068218 TTAACATTACAAAATT-
1 TTAAC-TTATAAAATTA
5068234 TTAACTTATAAAATTA
1 TTAACTTATAAAATTA
5068250 TTAA-TTATAA
1 TTAACTTATAA
5068260 TGTATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:5069110 original size:33 final size:33
Alignment explanation
Indices: 5069068--5069151 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
5069058 TGGTGGGTCA
*
5069068 TGGAGCAAGGGTCTCTAGCCTAGTGGACGGAAC
1 TGGAGCAAGGGTCTCTAGCCTAGTGGAAGGAAC
* *
5069101 TGGAGCAAGGGTCTCTGGCTTAGTGGAAGGAAC
1 TGGAGCAAGGGTCTCTAGCCTAGTGGAAGGAAC
* *
5069134 -AGAGTAAGGGTCTC-AGCC
1 TGGAGCAAGGGTCTCTAGCC
5069152 CCAGTGGAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 2 0.05
32 12 0.27
33 30 0.68
ACGTcount: A:0.25, C:0.19, G:0.37, T:0.19
Consensus pattern (33 bp):
TGGAGCAAGGGTCTCTAGCCTAGTGGAAGGAAC
Found at i:5080653 original size:49 final size:49
Alignment explanation
Indices: 5080597--5080691 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
5080587 AATTGTCACT
* *
5080597 ATGTTGTGGACATATGGAAAGATAGAGACATGATGGTCTTAGTGTGAAA
1 ATGTTGTGGACATATGAAAAAATAGAGACATGATGGTCTTAGTGTGAAA
*
5080646 ATGTTGTGGACATATGAAAAAATAGAGACATGATTGTCTTAGTGTG
1 ATGTTGTGGACATATGAAAAAATAGAGACATGATGGTCTTAGTGTG
5080692 GAATTGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (49 bp):
ATGTTGTGGACATATGAAAAAATAGAGACATGATGGTCTTAGTGTGAAA
Found at i:5093846 original size:76 final size:76
Alignment explanation
Indices: 5093720--5093865 Score: 258
Period size: 76 Copynumber: 1.9 Consensus size: 76
5093710 NNNNNNNNAC
* *
5093720 TATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTA-TGAATCACCTA
1 TATCCTTAATTTTAAGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTATTG-ATCACCCA
5093784 AAATTAAAATTT
65 AAATTAAAATTT
5093796 TATCCTTAATTTTAAGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTATTGATCACCCAA
1 TATCCTTAATTTTAAGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTATTGATCACCCAA
5093861 AATTA
66 AATTA
5093866 GAATAGATAG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
76 65 0.97
77 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (76 bp):
TATCCTTAATTTTAAGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTATTGATCACCCAA
AATTAAAATTT
Found at i:5094163 original size:21 final size:21
Alignment explanation
Indices: 5094122--5094164 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5094112 TTTTTTGCTG
*
5094122 CCAAACCCTTTTAAACACTCT
1 CCAAACCCTTCTAAACACTCT
*
5094143 CCAAACCCTCTCTCAAC-CTCT
1 CCAAACCCT-TCTAAACACTCT
5094164 C
1 C
5094165 AAGACACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (21 bp):
CCAAACCCTTCTAAACACTCT
Found at i:5101919 original size:1 final size:1
Alignment explanation
Indices: 5101913--5101941 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5101903 TTTTATCTTC
5101913 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5101942 GGTTTTGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5113469 original size:40 final size:40
Alignment explanation
Indices: 5113393--5113471 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
5113383 TTGGTTATTT
* *
5113393 TTCACCTTAATGGGATTTTCAACTTTGCCAAGATTGGTGA
1 TTCACCTTAATGGGATTTTCAACCTCGCCAAGATTGGTGA
*
5113433 TTCACCTTAGTGAGG-TTTTCAACCTCGCCACA-ATTGGTG
1 TTCACCTTAATG-GGATTTTCAACCTCGCCA-AGATTGGTG
5113472 TCCTTCGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (40 bp):
TTCACCTTAATGGGATTTTCAACCTCGCCAAGATTGGTGA
Found at i:5114569 original size:19 final size:20
Alignment explanation
Indices: 5114535--5114577 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
5114525 TTAAGTGATT
5114535 AATTTAAGTTATTTTAGTTA
1 AATTTAAGTTATTTTAGTTA
*
5114555 AATTTAAGTTA-TTTATTTA
1 AATTTAAGTTATTTTAGTTA
5114574 AATT
1 AATT
5114578 ACTTTAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
AATTTAAGTTATTTTAGTTA
Found at i:5121486 original size:22 final size:21
Alignment explanation
Indices: 5121415--5121567 Score: 101
Period size: 22 Copynumber: 6.9 Consensus size: 21
5121405 TCAGTCATAT
*
5121415 TGTTACACGCCATTTTCAAAAAA
1 TGTTACACG-CATGTTC-AAAAA
* * * *
5121438 TATTGCATGCTATGTTTAAAAAA
1 TGTTACACGC-ATG-TTCAAAAA
*
5121461 TGTTACACGTCATGTTCAAAAC
1 TGTTACACG-CATGTTCAAAAA
* *
5121483 TGTTACATGCAAGTTCAAAAAA
1 TGTTACACGCATGTTC-AAAAA
** *
5121505 TACTACACGCCATGTTCAAATA
1 TGTTACACG-CATGTTCAAAAA
5121527 TGTTACACGC-TAGTTCAAAAA
1 TGTTACACGCAT-GTTCAAAAA
*
5121548 TTGTTACATGCCATGTTCAA
1 -TGTTACACG-CATGTTCAA
5121568 TAAAAATGTT
Statistics
Matches: 99, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 15 0.15
22 44 0.44
23 35 0.35
24 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (21 bp):
TGTTACACGCATGTTCAAAAA
Found at i:5121519 original size:44 final size:43
Alignment explanation
Indices: 5121415--5121567 Score: 153
Period size: 44 Copynumber: 3.4 Consensus size: 43
5121405 TCAGTCATAT
* * * * *
5121415 TGTTACACGCCATTTTCAAAAAATATTGCATGCTATGTTTAAAAAA
1 TGTTACACGCCATGTTC--AAAATGTTACATGC-AAGTTCAAAAAA
*
5121461 TGTTACACGTCATGTTCAAAACTGTTACATGCAAGTTCAAAAAA
1 TGTTACACGCCATGTTCAAAA-TGTTACATGCAAGTTCAAAAAA
** * * *
5121505 TACTACACGCCATGTTCAAATATGTTACACGCTAGTTCAAAAAT
1 TGTTACACGCCATGTTCAAA-ATGTTACATGCAAGTTCAAAAAA
*
5121549 TGTTACATGCCATGTTCAA
1 TGTTACACGCCATGTTCAA
5121568 TAAAAATGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 66 0.73
45 9 0.10
46 15 0.17
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (43 bp):
TGTTACACGCCATGTTCAAAATGTTACATGCAAGTTCAAAAAA
Found at i:5121628 original size:41 final size:41
Alignment explanation
Indices: 5121576--5121672 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
5121566 AATAAAAATG
* * *
5121576 TTACATGCCATGTGCTAACACATGTTATTTCAGTATATTTT
1 TTACACGCCATGTGCTAACACATGTTATTTCAATATAGTTT
*
5121617 TTATACGCCATGTGCTAACACATGTTATTTCAATATAGTTT
1 TTACACGCCATGTGCTAACACATGTTATTTCAATATAGTTT
*
5121658 TTACATGCCATGTGC
1 TTACACGCCATGTGC
5121673 ATTATAGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (41 bp):
TTACACGCCATGTGCTAACACATGTTATTTCAATATAGTTT
Found at i:5122215 original size:20 final size:21
Alignment explanation
Indices: 5122183--5122227 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
5122173 ACAGTGGTTG
* *
5122183 AACAAATCAAAGACAAAACAA
1 AACAAATCAAAGAAAAAAAAA
5122204 AACAAA-CAAAGAAAAAAAAA
1 AACAAATCAAAGAAAAAAAAA
5122224 AACA
1 AACA
5122228 CCAAAACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.78, C:0.16, G:0.04, T:0.02
Consensus pattern (21 bp):
AACAAATCAAAGAAAAAAAAA
Found at i:5122387 original size:20 final size:21
Alignment explanation
Indices: 5122350--5122388 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5122340 AAACTCAAAG
*
5122350 GAGAAATCAAAAATTAGAATA
1 GAGAAAACAAAAATTAGAATA
5122371 GAGAAAACAAAAA-TAGAA
1 GAGAAAACAAAAATTAGAA
5122389 AGGATGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (21 bp):
GAGAAAACAAAAATTAGAATA
Found at i:5127883 original size:31 final size:31
Alignment explanation
Indices: 5127848--5127945 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
5127838 GAATTAGTTT
*
5127848 TTGGAGAATCGGTTTAAAAGCTATTCACATG
1 TTGGAGACTCGGTTTAAAAGCTATTCACATG
* ***
5127879 TTGGAGACTCGGTTTAAAAGCTTAAT-GGTTG
1 TTGGAGACTCGGTTTAAAAGC-TATTCACATG
** *
5127910 TTGGAGACTCAATTTAGAAGCTATTCACATG
1 TTGGAGACTCGGTTTAAAAGCTATTCACATG
5127941 TTGGA
1 TTGGA
5127946 CTTTTAACCA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 3 0.06
31 47 0.89
32 3 0.06
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (31 bp):
TTGGAGACTCGGTTTAAAAGCTATTCACATG
Found at i:5129301 original size:16 final size:15
Alignment explanation
Indices: 5129282--5129313 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5129272 ATTTTTGAGG
5129282 ATTTATTTATTTGTTT
1 ATTTATTTATTT-TTT
5129298 ATTTATTTATTTTTT
1 ATTTATTTATTTTTT
5129313 A
1 A
5129314 GGCAATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
ATTTATTTATTTTTT
Found at i:5141036 original size:2 final size:2
Alignment explanation
Indices: 5141031--5141055 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5141021 ATATATGATA
5141031 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5141056 AAACATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5149340 original size:168 final size:167
Alignment explanation
Indices: 5149054--5149383 Score: 493
Period size: 168 Copynumber: 2.0 Consensus size: 167
5149044 TCAACAGTTG
* *
5149054 ATGGAAGACTAAGATGAAGGCTAAAGAGGAAAAATAAGCTTTAGGATTTCTCTTCAGGCTTTTCC
1 ATGGAAGACTAAGATGAAGGCTAAAGAGGAAAAAAAAGCTTTAGAATTTCTCTTCAGGCTTTTCC
* *
5149119 AAGTGAGTGCTAGTCTTTTCTCTCTTCCAAATTACTTAAGGGCAACATTTTATAGCTAATGTGAA
66 AAGTGAGTGCTAGTCTTTTCTCCCTTCCAAATGACTTAAGGGCAACATTTTATAGCTAATGTGAA
5149184 GTTTGGAACCGTTAGACACAAGTTTGAATCAAAGCTTA
131 GTTTGG-ACCGTTAGACACAAGTTTGAATCAAAGCTTA
* * *
5149222 ATGGAAGACTAAGATGAAGGCTAACGAGGAAAAAAAAGCTTTTGAATTTCTCTTTAGTG-TTTTC
1 ATGGAAGACTAAGATGAAGGCTAAAGAGGAAAAAAAAGCTTTAGAATTTCTCTTCAG-GCTTTTC
* ** * * *
5149286 CAAGTGGGTGCTAGTCTTCTT-TCCCTTTTAAATGACTTAAGGGCAGCTTTTTATAGCTGATGTG
65 CAAGTGAGTGCTAGTCTT-TTCTCCCTTCCAAATGACTTAAGGGCAACATTTTATAGCTAATGTG
*
5149350 AAGTTTGGACTGTTAGACACAAGTTTGAATCAAA
129 AAGTTTGGACCGTTAGACACAAGTTTGAATCAAA
5149384 TCTGTCTGAA
Statistics
Matches: 146, Mismatches: 14, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
167 25 0.17
168 118 0.81
169 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (167 bp):
ATGGAAGACTAAGATGAAGGCTAAAGAGGAAAAAAAAGCTTTAGAATTTCTCTTCAGGCTTTTCC
AAGTGAGTGCTAGTCTTTTCTCCCTTCCAAATGACTTAAGGGCAACATTTTATAGCTAATGTGAA
GTTTGGACCGTTAGACACAAGTTTGAATCAAAGCTTA
Found at i:5149870 original size:19 final size:19
Alignment explanation
Indices: 5149846--5149892 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
5149836 ATTTGTAATA
5149846 AAAATTTAATTTTAATCCC
1 AAAATTTAATTTTAATCCC
5149865 AAAATTTAATTTTAATCCC
1 AAAATTTAATTTTAATCCC
5149884 AAAATTTAA
1 AAAATTTAA
5149893 ATTAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTAATTTTAATCCC
Found at i:5161294 original size:20 final size:20
Alignment explanation
Indices: 5161274--5161313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5161264 GTTAATAATA
5161274 TTAGTTTTATGTTATTTATAT
1 TTAGTTTTATGTT-TTTATAT
*
5161295 TTATTTTTATGTTTTTATA
1 TTAGTTTTATGTTTTTATA
5161314 GGAGTAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (20 bp):
TTAGTTTTATGTTTTTATAT
Found at i:5166978 original size:19 final size:19
Alignment explanation
Indices: 5166954--5166991 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5166944 TCCCTATAGT
5166954 GTCAGATTCGGGCACATAA
1 GTCAGATTCGGGCACATAA
*
5166973 GTCAGATTGGGGCACATAA
1 GTCAGATTCGGGCACATAA
5166992 TTTATTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (19 bp):
GTCAGATTCGGGCACATAA
Found at i:5168172 original size:21 final size:21
Alignment explanation
Indices: 5168141--5168194 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5168131 CAAAGAATAT
*
5168141 CTATGGATAGATGGCCCCCAC
1 CTATCGATAGATGGCCCCCAC
* *
5168162 CTA-CTGATAGATGGTCCCTAC
1 CTATC-GATAGATGGCCCCCAC
5168183 CTATCGATAGAT
1 CTATCGATAGAT
5168195 AGCAATTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
CTATCGATAGATGGCCCCCAC
Found at i:5173251 original size:18 final size:18
Alignment explanation
Indices: 5173224--5173262 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5173214 ATGCAAAAAG
*
5173224 AAAAAAAATA-GTTAGTC
1 AAAAAAAATAGGTTAGGC
5173241 AAAAGAAAATAGGTTAGGC
1 AAAA-AAAATAGGTTAGGC
5173260 AAA
1 AAA
5173263 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAAAAAATAGGTTAGGC
Found at i:5173941 original size:14 final size:14
Alignment explanation
Indices: 5173924--5173955 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5173914 ACTTAAAATT
*
5173924 AATTGATTAACTAA
1 AATTAATTAACTAA
5173938 AATTAATTAACTAA
1 AATTAATTAACTAA
5173952 AATT
1 AATT
5173956 TAAACGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (14 bp):
AATTAATTAACTAA
Done.