Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 25 of 27
Found at i:4390130 original size:3 final size:3
Alignment explanation
Indices: 4390118--4390155 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
4390108 TAATTAATTA
*
4390118 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4390156 TTTTATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:4395930 original size:7 final size:7
Alignment explanation
Indices: 4395893--4395927 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
4395883 TTATATTATA
4395893 TGGCACT
1 TGGCACT
4395900 TGGCACT
1 TGGCACT
4395907 TGGCACT
1 TGGCACT
*
4395914 TGGACACG
1 TGG-CACT
4395922 TGGCAC
1 TGGCAC
4395928 GTGCATGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (7 bp):
TGGCACT
Found at i:4398739 original size:21 final size:21
Alignment explanation
Indices: 4398715--4398755 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4398705 AAATATATTA
4398715 ATAAAAATAAATTTAAATTTG
1 ATAAAAATAAATTTAAATTTG
** *
4398736 ATAAATGTAATTTTAAATTT
1 ATAAAAATAAATTTAAATTT
4398756 ATTACCCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATAAAAATAAATTTAAATTTG
Found at i:4399238 original size:24 final size:24
Alignment explanation
Indices: 4399205--4399252 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4399195 TCTGAAGAAC
*
4399205 ACTTTAAGGAGATCCTTCAATTGT
1 ACTTTAAGGAGATCCTCCAATTGT
*
4399229 ACTTTCAGGAGATCCTCCAATTGT
1 ACTTTAAGGAGATCCTCCAATTGT
4399253 CTGGTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (24 bp):
ACTTTAAGGAGATCCTCCAATTGT
Found at i:4402938 original size:15 final size:14
Alignment explanation
Indices: 4402918--4402965 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 14
4402908 ATTTAGGTAA
4402918 AATATTATAAATATT
1 AATATTATAAAT-TT
4402933 AATATT-TAAATTT
1 AATATTATAAATTT
*
4402946 AAAATTAT---TTT
1 AATATTATAAATTT
4402957 AATATTATA
1 AATATTATA
4402966 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 10 0.34
13 7 0.24
14 6 0.21
15 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTATAAATTT
Found at i:4406565 original size:19 final size:20
Alignment explanation
Indices: 4406538--4406588 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4406528 TTATTTTTTT
*
4406538 ATATAATTATATAT-TAAAA
1 ATATTATTATATATATAAAA
*
4406557 ATATTATTAAATATATAAAA
1 ATATTATTATATATATAAAA
*
4406577 ATTTTA-TATATA
1 ATATTATTATATA
4406589 AATTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATTATATATATAAAA
Found at i:4406599 original size:15 final size:15
Alignment explanation
Indices: 4406566--4406608 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
4406556 AATATTATTA
*
4406566 AATATATAAAAATTT
1 AATATATATAAATTT
4406581 --TATATATAAATTT
1 AATATATATAAATTT
4406594 AATATAATATAAATT
1 AATAT-ATATAAATT
4406609 ATATCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 12 0.50
15 3 0.12
16 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATAAATTT
Found at i:4407695 original size:2 final size:2
Alignment explanation
Indices: 4407683--4407721 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4407673 ATCATGTACA
* *
4407683 AT AT AT A- AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4407722 CCTGATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4410709 original size:33 final size:33
Alignment explanation
Indices: 4410664--4410736 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
4410654 GTCTTCTTTG
*
4410664 TTTTTAACTTAATAATATTAAAAATAAATGTTA
1 TTTTTAACTTAATAATATTAAAAATAAATATTA
* * *
4410697 TTTTTAATTTAATAATATTGATAATAAATATTA
1 TTTTTAACTTAATAATATTAAAAATAAATATTA
4410730 TTTTTAA
1 TTTTTAA
4410737 AATTTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (33 bp):
TTTTTAACTTAATAATATTAAAAATAAATATTA
Found at i:4413586 original size:21 final size:21
Alignment explanation
Indices: 4413560--4413603 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4413550 TTGATGAATG
4413560 ATAATTTCACAAGTCAGTTTT
1 ATAATTTCACAAGTCAGTTTT
4413581 ATAATTTCACAAGTCAGTTTT
1 ATAATTTCACAAGTCAGTTTT
4413602 AT
1 AT
4413604 TGCTTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
ATAATTTCACAAGTCAGTTTT
Found at i:4421761 original size:8 final size:9
Alignment explanation
Indices: 4421743--4421767 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4421733 ATTATTTTAT
4421743 AAAATTAAA
1 AAAATTAAA
4421752 AAAATTAAA
1 AAAATTAAA
4421761 AAAATTA
1 AAAATTA
4421768 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:4423890 original size:3 final size:3
Alignment explanation
Indices: 4423882--4423929 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
4423872 ATATAGCGTC
*
4423882 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4423930 CTTTTGTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4423961 original size:2 final size:2
Alignment explanation
Indices: 4423954--4424000 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
4423944 TTTTTAGTTT
*
4423954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
4423997 TA TA
1 TA TA
4424001 ATCATGTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4424447 original size:18 final size:18
Alignment explanation
Indices: 4424420--4424468 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4424410 ACTTTTAAAC
4424420 TTTTATTAATTTGTATTGTA
1 TTTTA-TAATTT-TATTGTA
* *
4424440 -TTTATAATTTTTTTTTA
1 TTTTATAATTTTATTGTA
4424457 TTTTATAATTTT
1 TTTTATAATTTT
4424469 TATTAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 17 0.65
19 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTTATAATTTTATTGTA
Found at i:4425890 original size:24 final size:25
Alignment explanation
Indices: 4425857--4425932 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 25
4425847 ATAAAAATTT
* *
4425857 ACCACTATTTTTTACAAACAACA-A
1 ACCACCATTTTTTACAAACAAAAGA
* *
4425881 ATCACCATTTTTGACAAACACAAAAGA
1 ACCACCATTTTTTAC-AA-ACAAAAGA
4425908 ACCACCATTTTTTACAAACATAAAG
1 ACCACCATTTTTTACAAACA-AAAG
4425933 GGTGACCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 12 0.29
25 5 0.12
26 11 0.26
27 14 0.33
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (25 bp):
ACCACCATTTTTTACAAACAAAAGA
Found at i:4429625 original size:24 final size:24
Alignment explanation
Indices: 4429598--4429653 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
4429588 CCATCCTCCC
* *
4429598 CCATTTTATAATAAA-AATGAGCCA
1 CCATTTT-TAACAAACAATAAGCCA
*
4429622 CCATTTTTGACAAACAATAAGCCA
1 CCATTTTTAACAAACAATAAGCCA
4429646 CCATTTTT
1 CCATTTTT
4429654 TATAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (24 bp):
CCATTTTTAACAAACAATAAGCCA
Found at i:4431212 original size:24 final size:24
Alignment explanation
Indices: 4431172--4431233 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
4431162 ATTATAAATT
*
4431172 ATTTAAATATT-TGAATTAATTTTAA
1 ATTT-AATATTAT-AATTAATATTAA
* *
4431197 ATTTAATATTATAATTTATATTAT
1 ATTTAATATTATAATTAATATTAA
*
4431221 ATTTTATATTATA
1 ATTTAATATTATA
4431234 TAACCGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTAATATTATAATTAATATTAA
Found at i:4431234 original size:12 final size:12
Alignment explanation
Indices: 4431197--4431234 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4431187 TTAATTTTAA
*
4431197 ATTTAATATTAT
1 ATTTTATATTAT
*
4431209 AATTTATATTAT
1 ATTTTATATTAT
4431221 ATTTTATATTAT
1 ATTTTATATTAT
4431233 AT
1 AT
4431235 AACCGTAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTTATATTAT
Found at i:4432639 original size:35 final size:38
Alignment explanation
Indices: 4432585--4432657 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 38
4432575 TTTTTTTTTG
*
4432585 TATTTTTAGAATATCAGTATTGCTTAATTACTTTGTTC
1 TATTTTTAGAATATCAGTATTGCTTAATTACTGTGTTC
*
4432623 TATTTTTA-AAT-T-AGTATTGTTTAATTACTGTGTTC
1 TATTTTTAGAATATCAGTATTGCTTAATTACTGTGTTC
4432658 CACTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 21 0.64
36 1 0.03
37 3 0.09
38 8 0.24
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (38 bp):
TATTTTTAGAATATCAGTATTGCTTAATTACTGTGTTC
Found at i:4435308 original size:2 final size:2
Alignment explanation
Indices: 4435303--4435334 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4435293 TGTGTGTGTG
4435303 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
4435335 GCCATCCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4440022 original size:29 final size:33
Alignment explanation
Indices: 4439984--4440058 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
4439974 TATAATTTTA
4439984 TTTAAAATATT-AT-A-TAT-TTAAATATAAAT
1 TTTAAAATATTAATAATTATATTAAATATAAAT
* *
4440013 TTTAATATATTAATAATTTATATTATATATAAAT
1 TTTAAAATATTAATAA-TTATATTAAATATAAAT
4440047 TTTAAAAATATT
1 TTT-AAAATATT
4440059 CATTTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 10 0.27
30 2 0.05
31 1 0.03
33 3 0.08
34 14 0.38
35 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTAAAATATTAATAATTATATTAAATATAAAT
Found at i:4440050 original size:18 final size:16
Alignment explanation
Indices: 4440005--4440051 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
4439995 ATATATTTAA
4440005 ATATAAATTTTAATAT
1 ATATAAATTTTAATAT
*
4440021 AT-TAATAATTTATATTAT
1 ATAT-A-AATTT-TAATAT
4440039 ATATAAATTTTAA
1 ATATAAATTTTAA
4440052 AAATATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 1 0.04
16 5 0.20
17 10 0.40
18 8 0.32
19 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAAATTTTAATAT
Found at i:4449855 original size:2 final size:2
Alignment explanation
Indices: 4449848--4449880 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4449838 TGTATCATGC
4449848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4449881 AATAATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4450502 original size:22 final size:21
Alignment explanation
Indices: 4450476--4450539 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
4450466 CGTATTAATT
*
4450476 TTTATTTAATATTTTATTTTATA
1 TTTATTTAAT-TATT-TTTTATA
4450499 TTATATTTAATTATTTTTTATA
1 TT-TATTTAATTATTTTTTATA
* *
4450521 -TTATATAATTATATTTTAT
1 TTTATTTAATTATTTTTTAT
4450540 TTAAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 16 0.43
21 1 0.03
22 7 0.19
23 5 0.14
24 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTAATTATTTTTTATA
Found at i:4450529 original size:20 final size:21
Alignment explanation
Indices: 4450490--4450539 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
4450480 TTTAATATTT
4450490 TATTTTATATTATATTTAATTA
1 TATTTTATATTATA-TTAATTA
*
4450512 TTTTTTATATTATA-TAATTA
1 TATTTTATATTATATTAATTA
4450532 TATTTTAT
1 TATTTTAT
4450540 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.50
22 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTATATTATATTAATTA
Found at i:4451875 original size:24 final size:25
Alignment explanation
Indices: 4451824--4451881 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
4451814 TGGGTGGCTA
4451824 GTCAACAAAAGCCACCATTTGTGTTT
1 GTCAACAAAAGCCACCA-TTGTGTTT
4451850 GTCAACAAAAGCCACCA-TGTGTTT
1 GTCAACAAAAGCCACCATTGTGTTT
4451874 GTCAACAA
1 GTCAACAA
4451882 TGGTGGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 15 0.47
26 17 0.53
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
GTCAACAAAAGCCACCATTGTGTTT
Found at i:4451910 original size:27 final size:27
Alignment explanation
Indices: 4451871--4451936 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
4451861 CCACCATGTG
*
4451871 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
4451898 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
4451925 TTTGTCAAAAAT
1 TTTGTCAAAAAT
4451937 TATGACTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:4454540 original size:21 final size:22
Alignment explanation
Indices: 4454511--4454556 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
4454501 TGTTCAGACA
* *
4454511 AGTAGTACTCCGAAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4454533 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4454554 AGT
1 AGT
4454557 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:4456471 original size:24 final size:25
Alignment explanation
Indices: 4456420--4456477 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
4456410 TGGGTGGCTA
4456420 GTCAACAAAAGCCACCATTTGTGTTT
1 GTCAACAAAAGCCACCA-TTGTGTTT
4456446 GTCAACAAAAGCCACCA-TGTGTTT
1 GTCAACAAAAGCCACCATTGTGTTT
4456470 GTCAACAA
1 GTCAACAA
4456478 TGGTGGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 15 0.47
26 17 0.53
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
GTCAACAAAAGCCACCATTGTGTTT
Found at i:4456506 original size:27 final size:27
Alignment explanation
Indices: 4456467--4456532 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
4456457 CCACCATGTG
*
4456467 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
4456494 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
4456521 TTTGTCAAAAAT
1 TTTGTCAAAAAT
4456533 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:4456562 original size:24 final size:24
Alignment explanation
Indices: 4456494--4456563 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
4456484 TTACTTTGTA
* *
4456494 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
4456521 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
4456545 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
4456564 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:4457298 original size:20 final size:20
Alignment explanation
Indices: 4457273--4457317 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4457263 CGTTATTATT
4457273 ATATTAAAATATA-TATCATA
1 ATATTAAAATA-ACTATCATA
* *
4457293 ATATTAATATAACTATTATA
1 ATATTAAAATAACTATCATA
4457313 ATATT
1 ATATT
4457318 TAATTTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAAAATAACTATCATA
Found at i:4458162 original size:18 final size:18
Alignment explanation
Indices: 4458141--4458203 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
4458131 TAAATTTTAA
4458141 TATATTAATAATTTATAT
1 TATATTAATAATTTATAT
* * *
4458159 TATATATAA-ATTTTAAAA
1 TATAT-TAATAATTTATAT
* *
4458177 TAT-TTATTTATTTATAT
1 TATATTAATAATTTATAT
4458194 TATATTAATA
1 TATATTAATA
4458204 TTTTTTTTCA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
16 2 0.06
17 9 0.28
18 18 0.56
19 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTAATAATTTATAT
Found at i:4458171 original size:34 final size:34
Alignment explanation
Indices: 4458107--4458207 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 34
4458097 GTTATAATTT
* *
4458107 TATTTAATATATTATATTTAAATATAAATTTTAATA
1 TATTTAATAT-TTATA-TTATATATAAATTTTAAAA
4458143 TA-TTAATAATTTATATTATATATAAATTTTAAAA
1 TATTTAAT-ATTTATATTATATATAAATTTTAAAA
*
4458177 TATTTATTTATTTATATTATAT-TAATATTTT
1 TATTTA-ATATTTATATTATATATAA-ATTTT
4458208 TTTTCATATC
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
34 22 0.38
35 31 0.53
36 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TATTTAATATTTATATTATATATAAATTTTAAAA
Found at i:4458179 original size:16 final size:16
Alignment explanation
Indices: 4458128--4458179 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
4458118 TTATATTTAA
4458128 ATATAAATTTTAATAT
1 ATATAAATTTTAATAT
*
4458144 AT-TAATAATTTATATTAT
1 ATAT-A-AATTT-TAATAT
*
4458162 ATATAAATTTTAAAAT
1 ATATAAATTTTAATAT
4458178 AT
1 AT
4458180 TTATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
15 1 0.03
16 9 0.31
17 10 0.34
18 8 0.28
19 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAAATTTTAATAT
Found at i:4458221 original size:23 final size:22
Alignment explanation
Indices: 4458187--4458246 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
4458177 TATTTATTTA
4458187 TTTATATTATATTAATATTTTT
1 TTTATATTATATTAATATTTTT
* * *
4458209 TTTCATATCATATTTATATTATTA
1 TTT-ATATTATATTAATATT-TTT
4458233 TTTATATTATATTA
1 TTTATATTATATTA
4458247 GTTTCTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 3 0.10
23 23 0.74
24 5 0.16
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATATTATATTAATATTTTT
Found at i:4458258 original size:18 final size:17
Alignment explanation
Indices: 4458180--4458246 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 17
4458170 TTTAAAATAT
4458180 TTATTTAT-TTATATTA
1 TTATTTATATTATATTA
* *
4458196 -TATTAATATT-T-TTT
1 TTATTTATATTATATTA
*
4458210 TTCATATCATATTTATATTA
1 TT-AT-TTATA-TTATATTA
4458230 TTATTTATATTATATTA
1 TTATTTATATTATATTA
4458247 GTTTCTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
14 2 0.05
15 8 0.21
16 4 0.10
17 12 0.31
18 6 0.15
19 3 0.08
20 4 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTATATTATATTA
Found at i:4459614 original size:16 final size:16
Alignment explanation
Indices: 4459595--4459631 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
4459585 ATGATTGCAA
4459595 TTTAAAATCTTTT-TT
1 TTTAAAATCTTTTATT
*
4459610 TTTTAAATCTTTTATT
1 TTTAAAATCTTTTATT
4459626 TTTAAA
1 TTTAAA
4459632 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAAAATCTTTTATT
Found at i:4459617 original size:15 final size:15
Alignment explanation
Indices: 4459599--4459641 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4459589 TTGCAATTTA
4459599 AAATCTTTTTTTTTT
1 AAATCTTTTTTTTTT
*
4459614 AAATCTTTTATTTTT
1 AAATCTTTTTTTTTT
4459629 AAA-CTTATTTTTT
1 AAATCTT-TTTTTT
4459642 AACCTTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
AAATCTTTTTTTTTT
Found at i:4463694 original size:12 final size:12
Alignment explanation
Indices: 4463679--4463706 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4463669 AGAGAGCGAG
4463679 AGAGACAGAGAC
1 AGAGACAGAGAC
4463691 AGAGACAGAGAC
1 AGAGACAGAGAC
4463703 AGAG
1 AGAG
4463707 GGTATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.14, G:0.36, T:0.00
Consensus pattern (12 bp):
AGAGACAGAGAC
Found at i:4469501 original size:22 final size:21
Alignment explanation
Indices: 4469444--4469502 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 21
4469434 AAGTTTCCCA
4469444 TGATTTTTCTTGTCTTT--AT
1 TGATTTTTCTTGTCTTTGGAT
* * * *
4469463 T-ATTTTTTTTTTTTTTGGTT
1 TGATTTTTCTTGTCTTTGGAT
4469483 CTGATTTTTCTTGTCTTTGG
1 -TGATTTTTCTTGTCTTTGG
4469503 GTACTAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 12 0.41
19 1 0.03
20 1 0.03
21 1 0.03
22 14 0.48
ACGTcount: A:0.07, C:0.08, G:0.14, T:0.71
Consensus pattern (21 bp):
TGATTTTTCTTGTCTTTGGAT
Found at i:4470018 original size:26 final size:26
Alignment explanation
Indices: 4469985--4470036 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
4469975 TTACTTAATA
4469985 ATTTAATTTGT-TTAATT-TAAAAAAT
1 ATTTAATTT-TATTAATTATAAAAAAT
*
4470010 ATTTAAATTTTATTAGTTATAAAAAAT
1 ATTT-AATTTTATTAATTATAAAAAAT
4470037 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTAATTTTATTAATTATAAAAAAT
Found at i:4470049 original size:11 final size:11
Alignment explanation
Indices: 4470033--4470057 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4470023 TAGTTATAAA
4470033 AAATTTAAAAT
1 AAATTTAAAAT
4470044 AAATTTAAAAT
1 AAATTTAAAAT
4470055 AAA
1 AAA
4470058 ATATGTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:4475013 original size:28 final size:27
Alignment explanation
Indices: 4474962--4475029 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
4474952 ACCCATTTAG
*
4474962 TTGTAAAAAATGGTGGTTATTTTGTG-T
1 TTGTCAAAAATGGTGGTTATTTTG-GAT
*
4474989 TTGTCAAAAATGGTGGTTTTCTTTGGAT
1 TTGTCAAAAATGGTGGTTAT-TTTGGAT
*
4475017 TTGTCAAATATGG
1 TTGTCAAAAATGG
4475030 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (27 bp):
TTGTCAAAAATGGTGGTTATTTTGGAT
Found at i:4479263 original size:27 final size:28
Alignment explanation
Indices: 4479238--4479295 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
4479228 TTTATTTGTC
4479238 AAAATTGGTGGTTAT-TTTGTG-TTTGTCA
1 AAAA-TGGTGGTTATCTTTG-GATTTGTCA
*
4479266 AAAATGGTGGTTTTCTTTGGATTTGTCA
1 AAAATGGTGGTTATCTTTGGATTTGTCA
4479294 AA
1 AA
4479296 TATAGAGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.47
Consensus pattern (28 bp):
AAAATGGTGGTTATCTTTGGATTTGTCA
Found at i:4479284 original size:28 final size:27
Alignment explanation
Indices: 4479231--4479295 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
4479221 CCACCCATTT
*
4479231 ATTTGTCAAAATTGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTG-G
*
4479259 -TTTGTCAAAAATGGTGGTTTTCTTTGG
1 ATTTGTCAAAAATGGTGGTTAT-TTTGG
4479286 ATTTGTCAAA
1 ATTTGTCAAA
4479296 TATAGAGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 20 0.61
28 13 0.39
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (27 bp):
ATTTGTCAAAAATGGTGGTTATTTTGG
Found at i:4480249 original size:16 final size:16
Alignment explanation
Indices: 4480227--4480444 Score: 157
Period size: 16 Copynumber: 13.2 Consensus size: 16
4480217 AGCTCTAATA
4480227 AAAATAATTTTTATTT
1 AAAATAATTTTTATTT
*
4480243 GAAATAATTTTTATTT
1 AAAATAATTTTTATTT
** * *
4480259 AAAATAATTAATGTTC
1 AAAATAATTTTTATTT
*
4480275 AAAATAATTTTTATTG
1 AAAATAATTTTTATTT
*
4480291 AAAATAATTATTATTT
1 AAAATAATTTTTATTT
4480307 AAAATAACTATAATTTATATT
1 AAAATAA-T-T--TTTAT-TT
4480328 CAAAATAATTTTTATTT
1 -AAAATAATTTTTATTT
* * *
4480345 AAAATAATTTATGTTC
1 AAAATAATTTTTATTT
* * *
4480361 AATATAACTCTTATTT
1 AAAATAATTTTTATTT
* *** *
4480377 AAAATAGTTTACGTTC
1 AAAATAATTTTTATTT
** **
4480393 AAAGCAATTTACATTT
1 AAAATAATTTTTATTT
4480409 AAAATAATTTTTATTT
1 AAAATAATTTTTATTT
* *
4480425 CGAAATAATTTATATTT
1 -AAAATAATTTTTATTT
4480442 AAA
1 AAA
4480445 GCAACTCATG
Statistics
Matches: 153, Mismatches: 42, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
16 115 0.75
17 17 0.11
18 6 0.04
20 5 0.03
21 3 0.02
22 7 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (16 bp):
AAAATAATTTTTATTT
Found at i:4480319 original size:22 final size:22
Alignment explanation
Indices: 4480294--4480335 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4480284 TTTATTGAAA
*
4480294 ATAA-TTATTATTTAAAATAACT
1 ATAATTTA-TATTCAAAATAACT
4480316 ATAATTTATATTCAAAATAA
1 ATAATTTATATTCAAAATAA
4480336 TTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAATTTATATTCAAAATAACT
Found at i:4480333 original size:38 final size:38
Alignment explanation
Indices: 4480278--4480351 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
4480268 AATGTTCAAA
* *
4480278 ATAATTTTTATTGAAAATAATTATTATTTAAAATAACT
1 ATAATTTATATTCAAAATAATTATTATTTAAAATAACT
*
4480316 ATAATTTATATTCAAAATAATTTTTATTTAAAATAA
1 ATAATTTATATTCAAAATAATTATTATTTAAAATAA
4480352 TTTATGTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (38 bp):
ATAATTTATATTCAAAATAATTATTATTTAAAATAACT
Found at i:4480355 original size:48 final size:47
Alignment explanation
Indices: 4480227--4480355 Score: 114
Period size: 54 Copynumber: 2.6 Consensus size: 47
4480217 AGCTCTAATA
* * ** *
4480227 AAAATAATTTTTATTTGAAATAATTTTTATTTAAAATAATTAATGTTC
1 AAAATAATTTTTATTTAAAATAA-TTTAAAATAAAATAATTAATATTC
* * *
4480275 AAAATAATTTTTATTGAAAATAATTATTATTTAAAATAACTATAATTTATATTC
1 AAAATAATTTTTATT--TAA-AA-TA--ATTTAAAATAA-AATAATTAATATTC
4480329 AAAATAATTTTTATTTAAAATAATTTA
1 AAAATAATTTTTATTTAAAATAATTTA
4480356 TGTTCAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
48 20 0.31
50 3 0.05
51 4 0.06
52 4 0.06
53 7 0.11
54 27 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (47 bp):
AAAATAATTTTTATTTAAAATAATTTAAAATAAAATAATTAATATTC
Found at i:4482894 original size:21 final size:21
Alignment explanation
Indices: 4482817--4482905 Score: 62
Period size: 21 Copynumber: 4.3 Consensus size: 21
4482807 ATTTTATAAA
*
4482817 ATTTTATTTTATTAAATTAA--
1 ATTTTATTTTAATAAA-TAATT
*
4482837 ATTATTATTTTAAT---TATTT
1 ATT-TTATTTTAATAAATAATT
* *
4482856 ATATTATTTTTATAAAATAATT
1 ATTTTATTTTAAT-AAATAATT
*
4482878 ATTTTATTTTAATAAATAAAT
1 ATTTTATTTTAATAAATAATT
*
4482899 ATATTAT
1 ATTTTAT
4482906 AAATTATTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.04
18 9 0.17
19 2 0.04
20 3 0.06
21 22 0.42
22 15 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTATTTTAATAAATAATT
Found at i:4482926 original size:19 final size:19
Alignment explanation
Indices: 4482899--4482964 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
4482889 ATAAATAAAT
*
4482899 ATATTATAAATTATTAATA
1 ATATAATAAATTATTAATA
4482918 ATATAATAATGATTGATTAATA
1 ATATAATAA--ATT-ATTAATA
* *
4482940 ATATAATAAATGATTGATA
1 ATATAATAAATTATTAATA
*
4482959 ACATAA
1 ATATAA
4482965 CGAATAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 19 0.47
20 2 0.05
21 3 0.08
22 16 0.40
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (19 bp):
ATATAATAAATTATTAATA
Found at i:4482936 original size:22 final size:23
Alignment explanation
Indices: 4482911--4482957 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
4482901 ATTATAAATT
4482911 ATTAATAATATAAT-AATGATTG
1 ATTAATAATATAATAAATGATTG
4482933 ATTAATAATATAATAAATGATTG
1 ATTAATAATATAATAAATGATTG
4482956 AT
1 AT
4482958 AACATAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTAATAATATAATAAATGATTG
Found at i:4483079 original size:22 final size:21
Alignment explanation
Indices: 4483036--4483081 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4483026 AAATCACATA
* *
4483036 TTATAACTAAATTTTAATATT
1 TTATAACTAAATTATAAAATT
*
4483057 TTATAATTATAATTATAAAATT
1 TTATAACTA-AATTATAAAATT
4483079 TTA
1 TTA
4483082 CATAAGCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAACTAAATTATAAAATT
Found at i:4488871 original size:12 final size:12
Alignment explanation
Indices: 4488849--4488900 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
4488839 AACTGTGCCG
4488849 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
*
4488862 TCAATTTGAAACAG
1 TCAATTTG-AA-AT
*
4488876 TAAATTATGAAAT
1 TCAATT-TGAAAT
4488889 TCAATTTGAAAT
1 TCAATTTGAAAT
4488901 AGTGAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 10 0.31
13 12 0.38
14 8 0.25
15 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:4490576 original size:19 final size:19
Alignment explanation
Indices: 4490549--4490592 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
4490539 TAAATATCTT
*
4490549 TTATATTCAAATAAAATTA
1 TTATTTTCAAATAAAATTA
* *
4490568 TTATTTTCAACTTAAATTA
1 TTATTTTCAAATAAAATTA
4490587 TT-TTTT
1 TTATTTT
4490593 ATTAAATCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTTCAAATAAAATTA
Found at i:4491385 original size:26 final size:26
Alignment explanation
Indices: 4491349--4491407 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
4491339 TAGGCTGATT
4491349 GTGAAAATTTTTGTCAAATCATGCGA
1 GTGAAAATTTTTGTCAAATCATGCGA
4491375 GTGAAAATTTTTGTCAAATCATGCGA
1 GTGAAAATTTTTGTCAAATCATGCGA
4491401 GTGAAAA
1 GTGAAAA
4491408 GAATAGAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (26 bp):
GTGAAAATTTTTGTCAAATCATGCGA
Found at i:4495027 original size:24 final size:25
Alignment explanation
Indices: 4494954--4495026 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 25
4494944 AAACAAGCCT
* *
4494954 CCATATTTGACAAATCCAAAGAAAACCA
1 CCATTTTTGACAAA--CAAA-ATAACCA
4494982 CCATTTTTGACAAACATAAAATAACCA
1 CCATTTTTGACAAAC--AAAATAACCA
4495009 CCATTTTTGACAAACAAA
1 CCATTTTTGACAAACAAA
4495027 TGGGTGGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 21 0.51
28 16 0.39
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.23
Consensus pattern (25 bp):
CCATTTTTGACAAACAAAATAACCA
Found at i:4496941 original size:21 final size:22
Alignment explanation
Indices: 4496903--4496948 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4496893 TTCTGTTGAA
* **
4496903 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
4496924 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
4496946 ACT
1 ACT
4496949 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:4499425 original size:20 final size:20
Alignment explanation
Indices: 4499400--4499445 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4499390 AAGAATTGAA
*
4499400 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
4499420 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
4499440 GAGGGA
1 GAGGGA
4499446 ACCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:4506129 original size:27 final size:27
Alignment explanation
Indices: 4506098--4506170 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
4506088 AACCACACAT
*
4506098 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
4506125 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
4506152 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
4506171 CATGTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:4510799 original size:14 final size:13
Alignment explanation
Indices: 4510746--4510821 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
4510736 TACTTTTATT
4510746 TTATTTTAAATTAA
1 TTATTTT-AATTAA
* *
4510760 TTA--TTAAATAC
1 TTATTTTAATTAA
**
4510771 TTAAATTAACTTAA
1 TTATTTTAA-TTAA
4510785 TTATTTTAATATAA
1 TTATTTTAAT-TAA
*
4510799 TT-TTTAAATTAA
1 TTATTTTAATTAA
*
4510811 ATATTTTAATT
1 TTATTTTAATT
4510822 CAAATAATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
11 7 0.15
12 6 0.12
13 18 0.38
14 17 0.35
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTTAATTAA
Found at i:4511498 original size:17 final size:17
Alignment explanation
Indices: 4511473--4511536 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
4511463 TATTTTTATT
*
4511473 TTTATTTTTAAAATAAA
1 TTTAATTTTAAAATAAA
*
4511490 TTTAATTTTAAAAAAAA
1 TTTAATTTTAAAATAAA
*
4511507 TTTAAATTTTAAATTAAA
1 TTT-AATTTTAAAATAAA
*
4511525 TTTAAATTTAAA
1 TTTAATTTTAAA
4511537 TTTTTTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
17 26 0.63
18 15 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATTTTAAAATAAA
Found at i:4511503 original size:18 final size:18
Alignment explanation
Indices: 4511476--4511536 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
4511466 TTTTATTTTT
*
4511476 ATTTTTAAAATAAATTTA
1 ATTTTAAAAATAAATTTA
4511494 ATTTTAAAAA-AAATTTAA
1 ATTTTAAAAATAAATTT-A
*
4511512 ATTTT-AAATTAAATTTA
1 ATTTTAAAAATAAATTTA
*
4511529 AATTTAAA
1 ATTTTAAA
4511537 TTTTTTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 14 0.38
18 23 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAAAAATAAATTTA
Found at i:4511525 original size:5 final size:6
Alignment explanation
Indices: 4511486--4511539 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
4511476 ATTTTTAAAA
* * *
4511486 TAAATT TAATTT TAAA-A AAAATT TAAATTT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
4511533 TAAATT T
1 TAAATT T
4511540 TTTATTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 8 0.21
6 25 0.64
7 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:4511995 original size:13 final size:13
Alignment explanation
Indices: 4511977--4512007 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4511967 AGTATATTCA
4511977 TATATTTTAATAT
1 TATATTTTAATAT
*
4511990 TATATTTTAATTT
1 TATATTTTAATAT
4512003 TATAT
1 TATAT
4512008 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATATTTTAATAT
Found at i:4512015 original size:33 final size:38
Alignment explanation
Indices: 4511978--4512048 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
4511968 GTATATTCAT
4511978 ATATTTTA-ATAT-TATATTT-TAAT-T-TTATATAAA
1 ATATTTTATATATATATATTTATAATATATTATATAAA
*
4512011 ATATTTTATATTTATATATTTATAATATATTATATAAA
1 ATATTTTATATATATATATTTATAATATATTATATAAA
4512049 TTATAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 8 0.25
34 3 0.09
35 7 0.22
36 4 0.12
37 1 0.03
38 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
ATATTTTATATATATATATTTATAATATATTATATAAA
Found at i:4512016 original size:20 final size:20
Alignment explanation
Indices: 4511991--4512028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4511981 TTTTAATATT
4511991 ATATTTTA-ATTTTATATAAA
1 ATATTTTATA-TTTATATAAA
4512011 ATATTTTATATTTATATA
1 ATATTTTATATTTATATA
4512029 TTTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTATATTTATATAAA
Found at i:4512040 original size:11 final size:11
Alignment explanation
Indices: 4512024--4512074 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
4512014 TTTTATATTT
4512024 ATATATTTATA
1 ATATATTTATA
4512035 ATATA-TTAT-
1 ATATATTTATA
*
4512044 ATA-AATTATA
1 ATATATTTATA
4512054 ATATATTTATA
1 ATATATTTATA
*
4512065 TTATATTTAT
1 ATATATTTAT
4512075 GTCATATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 1 0.03
9 7 0.20
10 7 0.20
11 20 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATTTATA
Found at i:4512041 original size:19 final size:20
Alignment explanation
Indices: 4512001--4512065 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 20
4511991 ATATTTTAAT
* **
4512001 TTTATATAAAATATTTTATA
1 TTTATATAAATTATAATATA
*
4512021 TTTATAT-ATTTATAATATA
1 TTTATATAAATTATAATATA
4512040 -TTATATAAATTATAATATA
1 TTTATATAAATTATAATATA
4512059 TTTATAT
1 TTTATAT
4512066 TATATTTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 6 0.16
19 19 0.50
20 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATAAATTATAATATA
Found at i:4512059 original size:38 final size:35
Alignment explanation
Indices: 4511990--4512065 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 35
4511980 ATTTTAATAT
**
4511990 TATATTTTAATTTTATATAAAATATTTTATATTTA
1 TATATTTTAATTTTATATAAAATATAATATATTTA
*
4512025 TATATTTATAATATATTATATAAATTATAATATATTTA
1 TATATTT-TAAT-T-TTATATAAAATATAATATATTTA
4512063 TAT
1 TAT
4512066 TATATTTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 7 0.20
36 4 0.11
37 1 0.03
38 23 0.66
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TATATTTTAATTTTATATAAAATATAATATATTTA
Found at i:4516359 original size:23 final size:25
Alignment explanation
Indices: 4516323--4516372 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
4516313 TCAACTTGTA
4516323 ATCAGCTTAATGCTACTT-CTAAAG
1 ATCAGCTTAATGCTACTTACTAAAG
* *
4516347 ATCAG-TTTATGCTACTTATTAAAG
1 ATCAGCTTAATGCTACTTACTAAAG
4516371 AT
1 AT
4516373 AAAATACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (25 bp):
ATCAGCTTAATGCTACTTACTAAAG
Found at i:4521065 original size:3 final size:3
Alignment explanation
Indices: 4521057--4521083 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4521047 CTGCAAAAGT
4521057 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
4521084 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4524038 original size:2 final size:2
Alignment explanation
Indices: 4524031--4524059 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4524021 ACAAAGGTAA
4524031 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4524060 ATATTTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4524581 original size:141 final size:141
Alignment explanation
Indices: 4524327--4524607 Score: 526
Period size: 141 Copynumber: 2.0 Consensus size: 141
4524317 ATTTTTTCGA
*
4524327 ATTATCTTGCTGATTTTGTTGTTATCTTTCTGGAGTGCAACCATGAGCAAAGTTTTGAATTGAAA
1 ATTATCTTGCTGATTTTGTTGTTATCTTTCTGGAGTGCAACCATGAGCAAAGTTTTGAAGTGAAA
*
4524392 AGAGGCTTCTTAAGTAGTTGGAACATAACGAAGCTAAAACGAACTTACAGGAAACCGCTGCCAAA
66 AGAGGCTTCTTAAGTAGTTGAAACATAACGAAGCTAAAACGAACTTACAGGAAACCGCTGCCAAA
4524457 AGATCAGCTGT
131 AGATCAGCTGT
4524468 ATTATCTTGCTGATTTTGTTGTTATCTTTCTGGAGTGCAACCATGAGCAAAGTTTTGAAGTGAAA
1 ATTATCTTGCTGATTTTGTTGTTATCTTTCTGGAGTGCAACCATGAGCAAAGTTTTGAAGTGAAA
* *
4524533 AGAGGCTTTTTAAGTAGTTGAAACATAATGAAGCTAAAACGAACTTACAGGAAACCGCTGCCAAA
66 AGAGGCTTCTTAAGTAGTTGAAACATAACGAAGCTAAAACGAACTTACAGGAAACCGCTGCCAAA
4524598 AGATCAGCTG
131 AGATCAGCTG
4524608 CATTGGCCAA
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (141 bp):
ATTATCTTGCTGATTTTGTTGTTATCTTTCTGGAGTGCAACCATGAGCAAAGTTTTGAAGTGAAA
AGAGGCTTCTTAAGTAGTTGAAACATAACGAAGCTAAAACGAACTTACAGGAAACCGCTGCCAAA
AGATCAGCTGT
Found at i:4534533 original size:15 final size:15
Alignment explanation
Indices: 4534481--4534535 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
4534471 AGATGGAGGA
4534481 GAGGCATGAGGAAGAG
1 GAGG-ATGAGGAAGAG
*
4534497 GATGATGAGGAAGA-
1 GAGGATGAGGAAGAG
4534511 -A-GA--A-GAAGAG
1 GAGGATGAGGAAGAG
4534521 GAGGATGAGGAAGAG
1 GAGGATGAGGAAGAG
4534536 AATGAGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
9 5 0.16
10 1 0.03
11 1 0.03
12 4 0.12
13 1 0.03
14 1 0.03
15 16 0.50
16 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.47, T:0.07
Consensus pattern (15 bp):
GAGGATGAGGAAGAG
Found at i:4537024 original size:2 final size:2
Alignment explanation
Indices: 4537019--4537044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4537009 GCGTGTGTTT
4537019 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4537045 ACTTACAGTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4540664 original size:15 final size:15
Alignment explanation
Indices: 4540644--4540677 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4540634 TTTCATGCCA
4540644 GAAGAAGGATAT-GTG
1 GAAGAA-GATATCGTG
4540659 GAAGAAGATATCGTG
1 GAAGAAGATATCGTG
4540674 GAAG
1 GAAG
4540678 TCAAATCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.41, C:0.03, G:0.38, T:0.18
Consensus pattern (15 bp):
GAAGAAGATATCGTG
Found at i:4549737 original size:57 final size:57
Alignment explanation
Indices: 4549674--4549789 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
4549664 TCTTGATTCT
* *
4549674 TGCTTAAACAGTATAATTTTGTCCCAAAAGCACCACCATGTTTAAAGATTCATGTCA
1 TGCTTAAACAGTACAATTTTGTCCCAAAAACACCACCATGTTTAAAGATTCATGTCA
* * * *
4549731 TGCTTAAATAGTGCAATTTTGTCCCAAAAATACCGCCATGTTTAAAGATTCATGTCA
1 TGCTTAAACAGTACAATTTTGTCCCAAAAACACCACCATGTTTAAAGATTCATGTCA
4549788 TG
1 TG
4549790 AAAAAGACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (57 bp):
TGCTTAAACAGTACAATTTTGTCCCAAAAACACCACCATGTTTAAAGATTCATGTCA
Found at i:4550673 original size:2 final size:2
Alignment explanation
Indices: 4550666--4550700 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4550656 ACAGGCACAG
4550666 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4550701 AAGAAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4552173 original size:139 final size:139
Alignment explanation
Indices: 4551923--4552179 Score: 478
Period size: 139 Copynumber: 1.8 Consensus size: 139
4551913 TTAATATTCG
4551923 GAATTTCAACAATCATAGTTCTTTCCATACAAAGGTTGAAATGGCTGAAATGATGAAAATTACTT
1 GAATTTCAACAATCATAGTTCTTTCCATACAAAGGTTGAAATGGCTGAAATGATGAAAATTACTT
*
4551988 AGAATCTTCCCTTAGGTTGTCAATCAACATTAACTGCCTCTAAGATTTCTTGAATCTTTCCTTAA
66 AGAATCTTCCCTTAGGTTGTCAATCAACATTAACTGCCACTAAGATTTCTTGAATCTTTCCTTAA
4552053 TTATGCCCA
131 TTATGCCCA
4552062 GAATTTCAACAATCATAGTTCTTTCCATACAAAGGTTGAAATGGCTGAAATGATGAAAATTACTT
1 GAATTTCAACAATCATAGTTCTTTCCATACAAAGGTTGAAATGGCTGAAATGATGAAAATTACTT
* * *
4552127 AGATTCTTCCCTTTGGTTGTCAATCAGCATTAACTGCCACTAAGATTTCTTGA
66 AGAATCTTCCCTTAGGTTGTCAATCAACATTAACTGCCACTAAGATTTCTTGA
4552180 CTCTACCTTA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 114 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (139 bp):
GAATTTCAACAATCATAGTTCTTTCCATACAAAGGTTGAAATGGCTGAAATGATGAAAATTACTT
AGAATCTTCCCTTAGGTTGTCAATCAACATTAACTGCCACTAAGATTTCTTGAATCTTTCCTTAA
TTATGCCCA
Found at i:4553167 original size:31 final size:32
Alignment explanation
Indices: 4553131--4553198 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
4553121 TAATAAAATA
** *
4553131 AAATTTTTAAATTGAT-CATATTTAATTAATT
1 AAATTTTTAAATAAATAAATATTTAATTAATT
*
4553162 AAA-TTTTAAATAAATAAATTTTTAATTAATT
1 AAATTTTTAAATAAATAAATATTTAATTAATT
4553193 AAATTT
1 AAATTT
4553199 AATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 10 0.32
31 19 0.61
32 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
AAATTTTTAAATAAATAAATATTTAATTAATT
Found at i:4553169 original size:15 final size:15
Alignment explanation
Indices: 4553151--4553207 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
4553141 ATTGATCATA
4553151 TTTAATTAATTAAAT
1 TTTAATTAATTAAAT
* *
4553166 TTTAAATAAATAAATT
1 TTTAATTAATTAAA-T
4553182 TTTAATTAATTAAA-
1 TTTAATTAATTAAAT
4553196 TTTAATTTAATT
1 TTTAA-TTAATT
4553208 TGATAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.14
15 18 0.50
16 13 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTAATTAAAT
Found at i:4553680 original size:15 final size:15
Alignment explanation
Indices: 4553643--4553680 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4553633 AAATTATATT
4553643 TTTTAAAAAATTAAA
1 TTTTAAAAAATTAAA
* *
4553658 ATTAAAAAAATTAAA
1 TTTTAAAAAATTAAA
4553673 TTTTAAAA
1 TTTTAAAA
4553681 TGAATAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTTAAAAAATTAAA
Found at i:4557152 original size:17 final size:17
Alignment explanation
Indices: 4557130--4557162 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4557120 AAGTTTGGAT
4557130 TTTGAT-TGATATTTACA
1 TTTGATATGAT-TTTACA
4557147 TTTGATATGATTTTAC
1 TTTGATATGATTTTAC
4557163 GATCTTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (17 bp):
TTTGATATGATTTTACA
Found at i:4558945 original size:27 final size:28
Alignment explanation
Indices: 4558884--4558953 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
4558874 AAACAAGCCT
*
4558884 CCATATTTGACAAATCCAAAGAAAACCA
1 CCATTTTTGACAAATCCAAAGAAAACCA
*
4558912 CCATTTTTGACAAA-CACAAA-ATAACCA
1 CCATTTTTGACAAATC-CAAAGAAAACCA
4558939 CCATTTTTGACAAAT
1 CCATTTTTGACAAAT
4558954 AAATGGGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAATCCAAAGAAAACCA
Found at i:4562206 original size:214 final size:214
Alignment explanation
Indices: 4561837--4562268 Score: 855
Period size: 214 Copynumber: 2.0 Consensus size: 214
4561827 CTGATAGTAA
4561837 TACAAGTTATTTTTTCTGATGCCCTTCATTATCACGAGTGCTCCAGATGTGACCTTTAAAACTCC
1 TACAAGTTATTTTTTCTGATGCCCTTCATTATCACGAGTGCTCCAGATGTGACCTTTAAAACTCC
4561902 ATCTCTTAAAGTGATGACTGAGCCTTTGGATTCTAAGGCTCCCAACGAGATAAGATTTTTCTTCA
66 ATCTCTTAAAGTGATGACTGAGCCTTTGGATTCTAAGGCTCCCAACGAGATAAGATTTTTCTTCA
4561967 AACTGGGCACGTAACGGACATCATTCAGAACTCTAGTTGATCCATCTTGATTCTTCAATCGGATT
131 AACTGGGCACGTAACGGACATCATTCAGAACTCTAGTTGATCCATCTTGATTCTTCAATCGGATT
4562032 GAACATATCCCAACAGTTT
196 GAACATATCCCAACAGTTT
*
4562051 TACAAGTTATTTTTTCTGATGTCCTTCATTATCACGAGTGCTCCAGATGTGACCTTTAAAACTCC
1 TACAAGTTATTTTTTCTGATGCCCTTCATTATCACGAGTGCTCCAGATGTGACCTTTAAAACTCC
4562116 ATCTCTTAAAGTGATGACTGAGCCTTTGGATTCTAAGGCTCCCAACGAGATAAGATTTTTCTTCA
66 ATCTCTTAAAGTGATGACTGAGCCTTTGGATTCTAAGGCTCCCAACGAGATAAGATTTTTCTTCA
4562181 AACTGGGCACGTAACGGACATCATTCAGAACTCTAGTTGATCCATCTTGATTCTTCAATCGGATT
131 AACTGGGCACGTAACGGACATCATTCAGAACTCTAGTTGATCCATCTTGATTCTTCAATCGGATT
4562246 GAACATATCCCAACAGTTT
196 GAACATATCCCAACAGTTT
4562265 TACA
1 TACA
4562269 GGTGTTGTCA
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 217 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (214 bp):
TACAAGTTATTTTTTCTGATGCCCTTCATTATCACGAGTGCTCCAGATGTGACCTTTAAAACTCC
ATCTCTTAAAGTGATGACTGAGCCTTTGGATTCTAAGGCTCCCAACGAGATAAGATTTTTCTTCA
AACTGGGCACGTAACGGACATCATTCAGAACTCTAGTTGATCCATCTTGATTCTTCAATCGGATT
GAACATATCCCAACAGTTT
Found at i:4565580 original size:1 final size:1
Alignment explanation
Indices: 4565576--4565601 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4565566 TTTTTTTTTT
4565576 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
4565602 TACAAGACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4566629 original size:2 final size:2
Alignment explanation
Indices: 4566622--4566647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4566612 ACTTTAAAGA
4566622 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
4566648 GAGGAATAAT
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:4566788 original size:2 final size:2
Alignment explanation
Indices: 4566781--4566814 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4566771 ATCAGTTCTA
4566781 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4566815 ACCTCTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4570277 original size:3 final size:3
Alignment explanation
Indices: 4570269--4570297 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4570259 TTGAAACAAA
4570269 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4570298 AAAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4578879 original size:22 final size:21
Alignment explanation
Indices: 4578844--4578888 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
4578834 ATTAACTTTT
* *
4578844 AATTTTATTTATAAAATTTAA
1 AATTTTATTAATAAAATATAA
*
4578865 AATTTGTATTAATAATATATAA
1 AATTT-TATTAATAAAATATAA
4578887 AA
1 AA
4578889 GATCGTCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTTTATTAATAAAATATAA
Found at i:4580435 original size:4 final size:4
Alignment explanation
Indices: 4580426--4580479 Score: 60
Period size: 4 Copynumber: 13.5 Consensus size: 4
4580416 CTTCTTTCAG
4580426 TTCT TTC- TT-T TTCT TTCT CTTCT TTCTT TTCT TTCT TTCT TT-T TGTCT
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTC-T TTCT TTCT TTCT TTCT T-TCT
4580474 TTCT TT
1 TTCT TT
4580480 GTCTATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.14
4 28 0.64
5 10 0.23
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:4580439 original size:19 final size:18
Alignment explanation
Indices: 4580417--4580460 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
4580407 TTCTCCTACC
*
4580417 TTCTTTCAGTTCTTTCTTT
1 TTCTTTCACTTCTTTC-TT
*
4580436 TTCTTTCTCTTCTTTCTT
1 TTCTTTCACTTCTTTCTT
4580454 TTCTTTC
1 TTCTTTC
4580461 TTTCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.70
Consensus pattern (18 bp):
TTCTTTCACTTCTTTCTT
Found at i:4580448 original size:9 final size:9
Alignment explanation
Indices: 4580416--4580467 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
4580406 TTTCTCCTAC
*
4580416 CTTCTTTCA
1 CTTCTTTCT
*
4580425 GTTCTTTCTT
1 CTTCTTTC-T
*
4580435 TTTCTTTCT
1 CTTCTTTCT
4580444 CTTCTTTCT
1 CTTCTTTCT
*
4580453 TTTCTTTCT
1 CTTCTTTCT
4580462 -TTCTTT
1 CTTCTTT
4580468 TTGTCTTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
8 6 0.16
9 24 0.65
10 7 0.19
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (9 bp):
CTTCTTTCT
Found at i:4580458 original size:12 final size:12
Alignment explanation
Indices: 4580429--4580479 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
4580419 CTTTCAGTTC
4580429 TTTCTT-TTTCT
1 TTTCTTCTTTCT
4580440 TTCTCTTCTTTCT
1 TT-TCTTCTTTCT
4580453 TTTCTTTCTTTCT
1 TTTC-TTCTTTCT
4580466 TTT-TGTCTTTCT
1 TTTCT-TCTTTCT
4580478 TT
1 TT
4580480 GTCTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.08
12 15 0.42
13 18 0.50
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTCTTCTTTCT
Found at i:4582996 original size:21 final size:21
Alignment explanation
Indices: 4582971--4583012 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4582961 ATAAATCAAA
*
4582971 AGTAAATCGCAATTATAATTG
1 AGTAAATAGCAATTATAATTG
*
4582992 AGTAAATAGTAATTATAATTG
1 AGTAAATAGCAATTATAATTG
4583013 TGTCTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (21 bp):
AGTAAATAGCAATTATAATTG
Found at i:4589026 original size:3 final size:3
Alignment explanation
Indices: 4589018--4589066 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
4589008 ATTTTAAAAC
* *
4589018 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4589066 T
1 T
4589067 CAAAATGACG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4589763 original size:129 final size:129
Alignment explanation
Indices: 4589526--4589786 Score: 407
Period size: 129 Copynumber: 2.0 Consensus size: 129
4589516 GAGTCAATGG
** **
4589526 CATGAATCAGATGATATTCATAGCACCAAAGCTGACAAAAACCACACCGGCCAGCAGTGATGAAA
1 CATGAATCAGATGATATTCATAGCACCAAAGCTGACAAAAACCACACCGGCCAGCAGCAACAAAA
* *
4589591 ACAGTGGTGTTGTGACGATTACCTTTTCTATTTCCCTTTATTTCTAGTTCTTTCTATTCTCAGC
66 ACAGTGGTGTCGTGACGATTACCTTTTCTATTTCCCTTTATTTCTAGTTCCTTCTATTCTCAGC
** * *
4589655 CATGAATCAGATGATATTCATAGCACCTCAGCTGACAGAAACCACAGCGGCCAGCAGCAACAAAA
1 CATGAATCAGATGATATTCATAGCACCAAAGCTGACAAAAACCACACCGGCCAGCAGCAACAAAA
*
4589720 ACAGTGGTGTCGTGACGATTACCTTTTCTATTT-CCTTTCATTTCTAGTTCCTTCTATTCTGAGC
66 ACAGTGGTGTCGTGACGATTACCTTTTCTATTTCCCTTT-ATTTCTAGTTCCTTCTATTCTCAGC
4589784 CAT
1 CAT
4589787 CTTTGACTAG
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
128 5 0.04
129 115 0.96
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (129 bp):
CATGAATCAGATGATATTCATAGCACCAAAGCTGACAAAAACCACACCGGCCAGCAGCAACAAAA
ACAGTGGTGTCGTGACGATTACCTTTTCTATTTCCCTTTATTTCTAGTTCCTTCTATTCTCAGC
Found at i:4595512 original size:2 final size:2
Alignment explanation
Indices: 4595507--4595538 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4595497 TATCAAATTC
4595507 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4595539 CTCCATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4598729 original size:14 final size:14
Alignment explanation
Indices: 4598710--4598736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4598700 CCCTACCGAA
4598710 AAAGGAAAAAAGAG
1 AAAGGAAAAAAGAG
4598724 AAAGGAAAAAAGA
1 AAAGGAAAAAAGA
4598737 AGATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGGAAAAAAGAG
Found at i:4599301 original size:2 final size:2
Alignment explanation
Indices: 4599274--4599319 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
4599264 CCTTTTATTC
* * * *
4599274 AT AT AC AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4599316 AT AT
1 AT AT
4599320 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:4599319 original size:8 final size:8
Alignment explanation
Indices: 4599274--4599318 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
4599264 CCTTTTATTC
4599274 ATATACAT
1 ATATACAT
4599282 ATATACAT
1 ATATACAT
*
4599290 ACATACAT
1 ATATACAT
*
4599298 ATATATAT
1 ATATACAT
*
4599306 ATATATAT
1 ATATACAT
4599314 ATATA
1 ATATA
4599319 TGTGTGTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATACAT
Found at i:4599324 original size:2 final size:2
Alignment explanation
Indices: 4599319--4599346 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4599309 TATATATATA
4599319 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4599347 CATATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4609452 original size:34 final size:34
Alignment explanation
Indices: 4609388--4609570 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
4609378 GGGGGGGGGG
* *
4609388 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
4609421 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
4609455 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
4609489 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
4609523 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
4609557 TGTTGATTAAATGG
1 TGTTGATTAAATGG
4609571 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:4614051 original size:34 final size:34
Alignment explanation
Indices: 4613985--4614169 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
4613975 AAGTGGGAGA
* *
4613985 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
4614018 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
4614052 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
4614086 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
4614120 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
4614154 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
4614170 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:4633380 original size:19 final size:19
Alignment explanation
Indices: 4633356--4633419 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
4633346 TTTCAACGAT
4633356 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
4633375 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
4633389 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
4633407 TTGTATCGATACA
1 TTGTATCGATACA
4633420 ATTTAAGCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:4633393 original size:32 final size:32
Alignment explanation
Indices: 4633357--4633421 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4633347 TTCAACGATT
4633357 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4633389 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4633421 T
1 T
4633422 TTAAGCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:4633394 original size:13 final size:13
Alignment explanation
Indices: 4633376--4633400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4633366 ACATAAGTGT
4633376 TGTATCGATACAA
1 TGTATCGATACAA
4633389 TGTATCGATACA
1 TGTATCGATACA
4633401 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4633482 original size:65 final size:65
Alignment explanation
Indices: 4633400--4633527 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
4633390 GTATCGATAC
*
4633400 ATAAGTGTTGTATCGATACAATTTAAGCTACTGCTAAAAAATATATCGATACATTACTCAACTAT
1 ATAAGTGTTGTATCGATACAATTTAAGCTACTGCCAAAAAATATATCGATACATTACTCAACTAT
* * *
4633465 ATAAGTTTTGTATCGATACAATTTAAGTTATTGCCAAAAAATATATCGATACATTACTCAACT
1 ATAAGTGTTGTATCGATACAATTTAAGCTACTGCCAAAAAATATATCGATACATTACTCAACT
4633528 GTATCGATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (65 bp):
ATAAGTGTTGTATCGATACAATTTAAGCTACTGCCAAAAAATATATCGATACATTACTCAACTAT
Found at i:4641499 original size:2 final size:2
Alignment explanation
Indices: 4641488--4641521 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4641478 ATAACATAAC
4641488 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4641522 AAACATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4644266 original size:2 final size:2
Alignment explanation
Indices: 4644248--4644286 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4644238 TTTTGCTTTC
* *
4644248 TA TA CA TA TA TA GA 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
4644287 GCATTTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4644562 original size:27 final size:28
Alignment explanation
Indices: 4644513--4644611 Score: 94
Period size: 32 Copynumber: 3.3 Consensus size: 28
4644503 TATGTAGATT
4644513 TATATTTATTATAATTATATTTAAAATATTA
1 TATATTTATTATAA--AT-TTTAAAATATTA
4644544 TATATTT-TTATAAATTTTAAAATATTA
1 TATATTTATTATAAATTTTAAAATATTA
4644571 -ATAATTTGTATTATATTAATTTTAAAATATTTA
1 TAT-A-TT-TATTATA--AATTTTAAAATA-TTA
*
4644604 TTTATTTA
1 TATATTTA
4644612 ACTTATATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
26 2 0.03
27 13 0.22
28 4 0.07
29 1 0.02
30 11 0.19
31 9 0.15
32 14 0.24
33 4 0.07
34 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TATATTTATTATAAATTTTAAAATATTA
Found at i:4644623 original size:33 final size:32
Alignment explanation
Indices: 4644556--4644623 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
4644546 TATTTTTATA
*
4644556 AATTTTAAAATATTAATAATTTGTATTATATT
1 AATTTTAAAATATTAATAATTTGAATTATATT
* *
4644588 AATTTTAAAATATTTATTTATTT-AACTTATATT
1 AATTTTAAAATA-TTAATAATTTGAA-TTATATT
4644621 AAT
1 AAT
4644624 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
AATTTTAAAATATTAATAATTTGAATTATATT
Found at i:4644638 original size:21 final size:24
Alignment explanation
Indices: 4644596--4644646 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 24
4644586 TTAATTTTAA
4644596 AATATTTATTTATTTAACTTATATT
1 AATA-TTATTTATTTAACTTATATT
4644621 AATATTATTT-TTT-A-TTATATT
1 AATATTATTTATTTAACTTATATT
4644642 -ATATT
1 AATATT
4644647 TTATGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 1 0.04
23 3 0.12
24 6 0.23
25 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
AATATTATTTATTTAACTTATATT
Found at i:4644642 original size:15 final size:16
Alignment explanation
Indices: 4644617--4644650 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4644607 ATTTAACTTA
*
4644617 TATTAATATTATTTTT
1 TATTAATATTATATTT
4644633 TATT-ATATTATATTT
1 TATTAATATTATATTT
4644648 TAT
1 TAT
4644651 GTTGTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATATTATATTT
Found at i:4646359 original size:44 final size:44
Alignment explanation
Indices: 4646295--4646424 Score: 224
Period size: 44 Copynumber: 3.0 Consensus size: 44
4646285 AACCTGAGAC
* *
4646295 GACCAGACAATAGAAAAAGATCTCAACTACACACATTGACCAAT
1 GACCAGACAATAGAAGAAGATCCCAACTACACACATTGACCAAT
4646339 GACCAGACAATAGAAGAAGATCCCAACTACACACATTGACCAAT
1 GACCAGACAATAGAAGAAGATCCCAACTACACACATTGACCAAT
* *
4646383 GACCAAACAATTGAAGAAGATCCCAACTACACACATTGACCA
1 GACCAGACAATAGAAGAAGATCCCAACTACACACATTGACCA
4646425 GACAACAATT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (44 bp):
GACCAGACAATAGAAGAAGATCCCAACTACACACATTGACCAAT
Found at i:4651082 original size:2 final size:2
Alignment explanation
Indices: 4651075--4651104 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4651065 CTGGTCAAAC
4651075 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4651105 TAAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4655014 original size:2 final size:2
Alignment explanation
Indices: 4655007--4655042 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4654997 AGGCAAAAAT
4655007 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4655043 GAGTGCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4657370 original size:12 final size:12
Alignment explanation
Indices: 4657340--4657373 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4657330 AAGTTCACCG
4657340 AAAAAAA-AAAA
1 AAAAAAACAAAA
4657351 AAAAAAACAAAA
1 AAAAAAACAAAA
*
4657363 CAAAAAACAAA
1 AAAAAAACAAA
4657374 CGTAAGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Done.