Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 8 of 27
Found at i:860540 original size:16 final size:17
Alignment explanation
Indices: 860456--860540 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 17
860446 AAATATGTAT
*
860456 ATATCAAAAT-TTAAATA
1 ATAT-AAAATATTATATA
*
860473 ATATAAATTATTA-AT-
1 ATATAAAATATTATATA
*
860488 GTATCAAAAT-TTATATAA
1 ATAT-AAAATATTATAT-A
*
860506 ATATAAAATATTTTA-A
1 ATATAAAATATTATATA
*
860522 ATAT-AATTATTATATA
1 ATATAAAATATTATATA
860538 ATA
1 ATA
860541 AAATATAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
15 14 0.26
16 21 0.39
17 12 0.22
18 7 0.13
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATAAAATATTATATA
Found at i:866913 original size:2 final size:2
Alignment explanation
Indices: 866906--866952 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
866896 GAGTGAAATA
866906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
866948 AT AT A
1 AT AT A
866953 CTAAAATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:867203 original size:12 final size:13
Alignment explanation
Indices: 867181--867209 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
867171 TTAAAATATA
867181 TTTATTTTTTATT
1 TTTATTTTTTATT
867194 TTTA-TTTTTATT
1 TTTATTTTTTATT
867206 TTTA
1 TTTA
867210 AACGTGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:867257 original size:20 final size:19
Alignment explanation
Indices: 867219--867257 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
867209 AAACGTGTAT
* *
867219 TTAATTAAAAATAATTTCA
1 TTAATAAAAAATAAGTTCA
867238 TTAATAAAAAATAAAGTTCA
1 TTAATAAAAAAT-AAGTTCA
867258 AAGCAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAATAAAAAATAAGTTCA
Found at i:867730 original size:11 final size:11
Alignment explanation
Indices: 867714--867739 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
867704 TCGTCAAGAT
867714 AAACCTACGCC
1 AAACCTACGCC
867725 AAACCTACGCC
1 AAACCTACGCC
867736 AAAC
1 AAAC
867740 TGTCCAAGAA
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:0.42, C:0.42, G:0.08, T:0.08
Consensus pattern (11 bp):
AAACCTACGCC
Found at i:873176 original size:21 final size:19
Alignment explanation
Indices: 873135--873172 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
873125 CAGGGGAAAA
873135 TATATTTAAAAAAATAAAT
1 TATATTTAAAAAAATAAAT
* *
873154 TATATTTACAAAATTAAAT
1 TATATTTAAAAAAATAAAT
873173 ATTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TATATTTAAAAAAATAAAT
Found at i:873869 original size:3 final size:3
Alignment explanation
Indices: 873861--873887 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
873851 CTTCCCAACT
873861 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
873888 TATATTCTTA
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):
ATA
Found at i:874136 original size:15 final size:15
Alignment explanation
Indices: 874097--874153 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
874087 TATCATATTT
874097 AATTATAATAAATATTAA
1 AATT-TAAT-AATA-TAA
*
874115 TATTTAATAATATAA
1 AATTTAATAATATAA
874130 AATTTAA-AATTATAA
1 AATTTAATAA-TATAA
874145 AATATTAAT
1 AAT-TTAAT
874154 TATAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.06
15 17 0.50
16 8 0.24
17 4 0.12
18 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTAATAATATAA
Found at i:874136 original size:22 final size:22
Alignment explanation
Indices: 874091--874162 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
874081 TTATGATATC
*
874091 ATATTTAATTATA-ATAAATATTA
1 ATATTTAATAATATA-AAAT-TTA
874114 ATATTTAATAATATAAAATTTA
1 ATATTTAATAATATAAAATTTA
* *
874136 AAATTATAA-AATAT-TAATTATA
1 ATATT-TAATAATATAAAATT-TA
874158 ATATT
1 ATATT
874163 ATATTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.10
22 18 0.43
23 19 0.45
24 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTTAATAATATAAAATTTA
Found at i:877675 original size:35 final size:35
Alignment explanation
Indices: 877629--877700 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
877619 TCGTAAATTT
*
877629 CAACCTTTTTTGCTCCTATGTTTCAAGAATTCTTA
1 CAACCTTTTTTGCTCCTATGTCTCAAGAATTCTTA
877664 CAACCTTTTTTGCTCCTATGTCTCAAGAATTCTTA
1 CAACCTTTTTTGCTCCTATGTCTCAAGAATTCTTA
877699 CA
1 CA
877701 CCTAATAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (35 bp):
CAACCTTTTTTGCTCCTATGTCTCAAGAATTCTTA
Found at i:883778 original size:3 final size:3
Alignment explanation
Indices: 883770--883806 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
883760 GGAAAAGAGG
*
883770 AGA AGA AGA AGA AGA AGA AGA AGA AGA ATA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
883807 CCCTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:884376 original size:22 final size:21
Alignment explanation
Indices: 884324--884376 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
884314 TTATAAAAAA
884324 TAATTTAAA-ATTTTATTATT
1 TAATTTAAATATTTTATTATT
*
884344 TAATTAAAAATATATTT-TTATT
1 TAATT-TAAATAT-TTTATTATT
884366 TAAATTTAAAT
1 T-AATTTAAAT
884377 TTAAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 3 0.11
22 12 0.44
23 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTTAAATATTTTATTATT
Found at i:884785 original size:19 final size:17
Alignment explanation
Indices: 884749--884788 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
884739 ATAATTATTA
884749 AATTATATAATAATAAT
1 AATTATATAATAATAAT
*
884766 AATTATAATCAATTATAAT
1 AATTAT-AT-AATAATAAT
884785 AATT
1 AATT
884789 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTATATAATAATAAT
Found at i:886212 original size:19 final size:20
Alignment explanation
Indices: 886171--886212 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
886161 ATTAAAAATT
* *
886171 TAAATTTTGTTAATTATAAA
1 TAAATTTTGTAAAATATAAA
*
886191 TAAATTTT-TAAAATATATA
1 TAAATTTTGTAAAATATAAA
886210 TAA
1 TAA
886213 TTAAATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAATTTTGTAAAATATAAA
Found at i:886984 original size:2 final size:2
Alignment explanation
Indices: 886979--887004 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
886969 TGTGTGTGTG
886979 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
887005 GGAGGCAAAT
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:890453 original size:30 final size:29
Alignment explanation
Indices: 890370--890453 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
890360 CGTTGAAATA
*
890370 AATTTTTAATTTATATCATAGTAAATTATT
1 AATTTTTAATTTATATCA-AATAAATTATT
* * * * *
890400 TATCTTTAAATTGTATCAAATAAATTCTT
1 AATTTTTAATTTATATCAAATAAATTATT
890429 AATTTTTAATTTATATCTAAATAAA
1 AATTTTTAATTTATATC-AAATAAA
890454 CTATCAACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTTTTAATTTATATCAAATAAATTATT
Found at i:891894 original size:29 final size:31
Alignment explanation
Indices: 891862--891927 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
891852 TAAATTTTTA
*
891862 ATTAAATTAAATACT-AAAACTTATTT-AAT
1 ATTAAATTAAAGACTAAAAACTTATTTGAAT
* *
891891 ATT-AATTAAAGATTAAAAATTTATTTGAAT
1 ATTAAATTAAAGACTAAAAACTTATTTGAAT
891921 A-TAAATT
1 ATTAAATT
891928 TAAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 9 0.29
29 14 0.45
30 8 0.26
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTAAATTAAAGACTAAAAACTTATTTGAAT
Found at i:891938 original size:29 final size:29
Alignment explanation
Indices: 891858--891943 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
891848 TTTTTAAATT
* * *
891858 TTTAAT-TAAATTAAATACT-AAAACTTA
1 TTTAATATAAATTAAAGATTAAAAATTTA
*
891885 TTTAATATTAATTAAAGATTAAAAATTTA
1 TTTAATATAAATTAAAGATTAAAAATTTA
891914 TTTGAATATAAATTTAAA-ATTAAAAATTTA
1 TTT-AATATAAA-TTAAAGATTAAAAATTTA
891944 CTCACTTTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 6 0.12
28 10 0.20
29 10 0.20
30 19 0.38
31 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTAATATAAATTAAAGATTAAAAATTTA
Found at i:892750 original size:24 final size:22
Alignment explanation
Indices: 892723--892781 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
892713 ATTCAATAAC
*
892723 ATAATTTAATAAAATTAAAGTTTT
1 ATAATTTAATAAAATT-AA-TTCT
892747 ATAATTTATATAAAAATTAATTCT
1 ATAATTTA-AT-AAAATTAATTCT
892771 A-AATTTAATAA
1 ATAATTTAATAA
892782 CCTAAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 6 0.19
24 12 0.38
25 4 0.12
26 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTAATAAAATTAATTCT
Found at i:892911 original size:2 final size:2
Alignment explanation
Indices: 892899--892938 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
892889 TTGCTTTTCA
* * *
892899 AT AT AT GT AT AT AT AT GT AT AT GT 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
892939 TAGATTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:892921 original size:16 final size:16
Alignment explanation
Indices: 892899--892936 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
892889 TTGCTTTTCA
892899 ATATATGTATATATAT
1 ATATATGTATATATAT
*
892915 GTATATGTATATATAT
1 ATATATGTATATATAT
892931 ATATAT
1 ATATAT
892937 ATTAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
ATATATGTATATATAT
Found at i:893471 original size:13 final size:12
Alignment explanation
Indices: 893453--893486 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
893443 TTTTAGAATT
893453 ATAATTTTAAAAA
1 ATAATTTT-AAAA
893466 ATAATTATTAAAA
1 ATAATT-TTAAAA
893479 ATAATTTT
1 ATAATTTT
893487 TCGTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATTTTAAAA
Found at i:893521 original size:28 final size:28
Alignment explanation
Indices: 893468--893521 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
893458 TTTAAAAAAT
*
893468 AATTATTAAAAATAATTTTTCGTTTTAA
1 AATTATTAAAAATAATTTTTCATTTTAA
* * *
893496 AATTTTTAAAGATAATTTTTTATTTT
1 AATTATTAAAAATAATTTTTCATTTT
893522 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (28 bp):
AATTATTAAAAATAATTTTTCATTTTAA
Found at i:899175 original size:18 final size:20
Alignment explanation
Indices: 899152--899190 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
899142 ATAATGAATT
*
899152 ATTTTAATATT-T-TAAATA
1 ATTTTAAGATTATGTAAATA
899170 ATTTTAAGATTATGTAAATA
1 ATTTTAAGATTATGTAAATA
899190 A
1 A
899191 ATTCATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTAAGATTATGTAAATA
Found at i:900060 original size:97 final size:96
Alignment explanation
Indices: 899844--900062 Score: 241
Period size: 96 Copynumber: 2.3 Consensus size: 96
899834 GAAACACTTT
* ** *
899844 AACCCCATTCCTCCGAAGAAATACTCTAACCTCGTTTTTAAACTTGTCAAGATTTAAATTATTTT
1 AACCCCATTCCTTCGAAGGGATACTCTAACCTCGTTTTTAAACTCGTCAAGATTTAAATTATTTT
899909 TTACTCAAATTATCATCATCGAAGACATTAC
66 TTACTCAAATTATCATCATCGAAGACATTAC
* * * *
899940 AATCACATT-CTTCCAAAGGGATACTTTAA-CTCCGTTTTTAAACTCGTCAAGATTTAAATCT-T
1 AACCCCATTCCTT-CGAAGGGATACTCTAACCT-CGTTTTTAAACTCGTCAAGATTTAAAT-TAT
* * * *
900002 ATTTTTGCTTAAA-TAGTCATTATCGAGGACA-TATC
63 -TTTTTACTCAAATTA-TCATCATCGAAGACATTA-C
900037 AACCCCATTCCTTCGAAGGGATACTC
1 AACCCCATTCCTTCGAAGGGATACTC
900063 CATCTCTATT
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
95 4 0.04
96 50 0.50
97 43 0.43
98 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (96 bp):
AACCCCATTCCTTCGAAGGGATACTCTAACCTCGTTTTTAAACTCGTCAAGATTTAAATTATTTT
TTACTCAAATTATCATCATCGAAGACATTAC
Found at i:900075 original size:97 final size:96
Alignment explanation
Indices: 899878--900075 Score: 206
Period size: 97 Copynumber: 2.1 Consensus size: 96
899868 TCTAACCTCG
* *
899878 TTTTTAAACTTGTCAAGATTTAAATTATTTTTTACTCAAATTATCATCATCGAAGACATTACAAT
1 TTTTTAAACTCGTCAAGATTTAAATTATTTTTTACTCAAATTATCATCATCGAAGACATTACAAC
** *
899943 CACATTCTTCCAAAGGGATACTTTAACTCCG
66 CACATTCTTCCAAAGGGATACTCCAACTCCA
* * * *
899974 TTTTTAAACTCGTCAAGATTTAAATCT-TATTTTTGCTTAAA-TAGTCATTATCGAGGACA-TAT
1 TTTTTAAACTCGTCAAGATTTAAAT-TAT-TTTTTACTCAAATTA-TCATCATCGAAGACATTA-
* * * *
900036 CAACCCCATTCCTT-CGAAGGGATACTCCATCTCTA
62 CAACCACATT-CTTCCAAAGGGATACTCCAACTCCA
900071 TTTTT
1 TTTTT
900076 CAATTAAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
96 29 0.35
97 52 0.62
98 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (96 bp):
TTTTTAAACTCGTCAAGATTTAAATTATTTTTTACTCAAATTATCATCATCGAAGACATTACAAC
CACATTCTTCCAAAGGGATACTCCAACTCCA
Found at i:901021 original size:22 final size:20
Alignment explanation
Indices: 900994--901044 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 20
900984 ATATTTTAAA
*
900994 ATTTAAATTTATTTATTATCT
1 ATTTAAATTTATATATTAT-T
901015 ATATTAAATTTATATATTATT
1 AT-TTAAATTTATATATTATT
901036 ATTTAAATT
1 ATTTAAATT
901045 CAAATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
21 5 0.18
22 16 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTAAATTTATATATTATT
Found at i:901620 original size:6 final size:6
Alignment explanation
Indices: 901609--901670 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
901599 TATAAAATTT
* *
901609 ATATAA ATATAA ATATAA A-AT-A ATTTAA ATATAA ATAT-G ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
901653 ATATAA TATATAA ATATA
1 ATATAA -ATATAA ATATA
901671 TTATGAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.04
5 11 0.23
6 29 0.60
7 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:901640 original size:22 final size:22
Alignment explanation
Indices: 901609--901670 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
901599 TATAAAATTT
901609 ATATAAATATAAATATAAAATA
1 ATATAAATATAAATATAAAATA
* * *
901631 ATTTAAATATAAATATGATATA
1 ATATAAATATAAATATAAAATA
901653 ATATAATATATAAATATA
1 ATATAA-ATATAAATATA
901671 TTATGAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATAAATATAAATATAAAATA
Found at i:901655 original size:10 final size:10
Alignment explanation
Indices: 901576--901681 Score: 58
Period size: 11 Copynumber: 10.2 Consensus size: 10
901566 TTTTTAAAAT
901576 TAATATAATA
1 TAATATAATA
901586 TGAATTATTAATA
1 T-AA-TA-TAATA
*
901599 T-ATAAAAT-
1 TAATATAATA
*
901607 TTATATAAATA
1 TAATAT-AATA
*
901618 TAAATATAAAA
1 T-AATATAATA
*
901629 TAATTTAAATA
1 TAATAT-AATA
*
901640 TAAATATGATA
1 T-AATATAATA
901651 TAATATAATA
1 TAATATAATA
901661 T-ATA-AATA
1 TAATATAATA
*
901669 TATTATGAATA
1 TAATAT-AATA
901680 TA
1 TA
901682 TAAATTATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
8 6 0.08
9 11 0.15
10 19 0.26
11 22 0.30
12 10 0.14
13 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (10 bp):
TAATATAATA
Found at i:901680 original size:29 final size:28
Alignment explanation
Indices: 901609--901694 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
901599 TATAAAATTT
*
901609 ATATAAATATAAATATAAAATAATTTAA
1 ATATAAATATGAATATAAAATAATTTAA
*
901637 ATATAAATATG-ATATAATATAATATATAA
1 ATATAAATATGAATATAAAATAAT-T-TAA
* *
901666 ATAT-ATTATGAATATATAAATTA-TTAA
1 ATATAAATATGAATATA-AAATAATTTAA
901693 AT
1 AT
901695 TTAACTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
27 16 0.33
28 17 0.35
29 12 0.24
30 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
ATATAAATATGAATATAAAATAATTTAA
Found at i:903677 original size:26 final size:26
Alignment explanation
Indices: 903648--903705 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
903638 TGTCTTCGAT
903648 GATAGAATCTTAAGTAATGAGGTCAG
1 GATAGAATCTTAAGTAATGAGGTCAG
903674 GATAGAATCTTAAGTAATGAGGTCAG
1 GATAGAATCTTAAGTAATGAGGTCAG
903700 GA-AGAA
1 GATAGAA
903706 AAGAAGCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.24
Consensus pattern (26 bp):
GATAGAATCTTAAGTAATGAGGTCAG
Found at i:907877 original size:108 final size:108
Alignment explanation
Indices: 907683--908008 Score: 589
Period size: 108 Copynumber: 3.0 Consensus size: 108
907673 GATGATACAT
*
907683 TATAATGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
1 TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
907748 ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
66 ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
907791 TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
1 TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
907856 ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
66 ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
* *
907899 TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTGAATTTCATTGAATTCAATCAGGTCATGGCA
1 TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
* * * *
907964 ATAGTGGATTTTTATATAATTGTTTCCTATTACATGACAACTG
66 ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
908007 TA
1 TA
908009 GGCATTAAAT
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 211 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (108 bp):
TATACTGTAAGAGGGGGTTGACCTCTTTATGCTTAAATTTAATTGAATTCAATCAGGTCATGGCA
ATAATGGATTTTTATATAATTGCTTCTTATCACATGACAACTG
Found at i:911832 original size:18 final size:17
Alignment explanation
Indices: 911805--911840 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
911795 TAATTACATG
*
911805 ATATAAAATATGATATA
1 ATATAAAATATAATATA
911822 ATATAAAAATATAATATA
1 ATAT-AAAATATAATATA
911840 A
1 A
911841 ACATAACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:911835 original size:13 final size:13
Alignment explanation
Indices: 911817--911841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
911807 ATAAAATATG
911817 ATATAATATAAAA
1 ATATAATATAAAA
911830 ATATAATATAAA
1 ATATAATATAAA
911842 CATAACATGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:912569 original size:21 final size:21
Alignment explanation
Indices: 912527--912566 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
912517 ATCCGGTTTT
912527 ATATAAATTACTATTTAATTA
1 ATATAAATTACTATTTAATTA
*
912548 ATATAAATTA-TTTTTAATT
1 ATATAAATTACTATTTAATT
912567 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAATTACTATTTAATTA
Found at i:917386 original size:2 final size:2
Alignment explanation
Indices: 917379--917403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
917369 ACTTTGCTAA
917379 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
917404 ACACCTTCTT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:919805 original size:18 final size:17
Alignment explanation
Indices: 919748--919805 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
919738 AATATATTCG
*
919748 ATAAATATAATAATTTTTA
1 ATAAATAAAATAA--TTTA
*
919767 ATATATAAAATAATTTAA
1 ATAAATAAAATAATTT-A
*
919785 ATAAATTAAATATATTTA
1 ATAAATAAAATA-ATTTA
919803 ATA
1 ATA
919806 TTAAACATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 15 0.45
19 15 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATAAAATAATTTA
Found at i:920441 original size:5 final size:5
Alignment explanation
Indices: 920418--920480 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
920408 ATATTTAAGC
* * *
920418 ATATT ATATC ATATT -TATT ATATT ATTTTT ATATT A-ATT A-AAT ATATT
1 ATATT ATATT ATATT ATATT ATATT A-TATT ATATT ATATT ATATT ATATT
*
920466 ATATTT TTATT ATAT
1 ATA-TT ATATT ATAT
920481 CTTTATTTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 11 0.24
5 27 0.59
6 8 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:920676 original size:5 final size:5
Alignment explanation
Indices: 920661--920712 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
920651 ATACACAGTT
*
920661 ATATAA ATATA ATATA A-ATA AAATA AT-TAA TATATA ATATA ATATA
1 ATAT-A ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
920707 ATATA A
1 ATATA A
920713 AATATTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
4 5 0.12
5 28 0.68
6 7 0.17
7 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:920901 original size:15 final size:15
Alignment explanation
Indices: 920878--920917 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
920868 TTTATTTTTA
*
920878 TTAAAATATTTATAT
1 TTAAAATATATATAT
*
920893 TTAATATATATATAT
1 TTAAAATATATATAT
*
920908 ATAAAATATA
1 TTAAAATATA
920918 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAATATATATAT
Found at i:922470 original size:2 final size:2
Alignment explanation
Indices: 922463--922497 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
922453 AAAGGATGAA
922463 AT 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 AT A
922498 AATTCAAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:922786 original size:29 final size:29
Alignment explanation
Indices: 922754--922822 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
922744 TAATGAAATC
* *
922754 TTTTAAAAGGTTATAGAAT-GTAAATATAA
1 TTTTAAAAGATTATA-AATAATAAATATAA
*
922783 TTTTAAAAAATTATAAATAAATAAATATAA
1 TTTTAAAAGATTATAAAT-AATAAATATAA
*
922813 TTTTTAAAGA
1 TTTTAAAAGA
922823 ATAAAATTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 3 0.09
29 13 0.39
30 17 0.52
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTTAAAAGATTATAAATAATAAATATAA
Found at i:925286 original size:20 final size:20
Alignment explanation
Indices: 925258--925297 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
925248 AGTTAAATAT
* *
925258 TTATTTTTATTAATTATTTA
1 TTATATTTAATAATTATTTA
*
925278 TTATATTTAATATTTATTTA
1 TTATATTTAATAATTATTTA
925298 ATATTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATTTAATAATTATTTA
Found at i:925290 original size:33 final size:34
Alignment explanation
Indices: 925223--925296 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
925213 ACGTTTTAAC
925223 TTTATTTTTAAAACTTATATTATTAAGTTAAATA
1 TTTATTTTTAAAACTTATATTATTAAGTTAAATA
* *
925257 TTTATTTTTATTAA-TTAT-TTATTATA-TTTAATA
1 TTTATTTTTA-AAACTTATATTATTA-AGTTAAATA
925290 TTTATTT
1 TTTATTT
925297 AATATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 19 0.53
34 15 0.42
35 2 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (34 bp):
TTTATTTTTAAAACTTATATTATTAAGTTAAATA
Found at i:925304 original size:17 final size:16
Alignment explanation
Indices: 925253--925326 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 16
925243 TATTAAGTTA
*
925253 AATATTTATTTTTATT
1 AATATTTATTTATATT
925269 AATTATTTA-TTATATTT
1 AA-TATTTATTTATA-TT
925286 AATATTTATTTAATATT
1 AATATTTATTT-ATATT
* *
925303 AAAATTATATTT-T-TA
1 AATATT-TATTTATATT
925318 AATATTTAT
1 AATATTTAT
925327 AATTTTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
14 3 0.06
15 6 0.12
16 13 0.27
17 19 0.39
18 8 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTATTTATATT
Found at i:925327 original size:16 final size:16
Alignment explanation
Indices: 925250--925334 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 16
925240 TATTATTAAG
*
925250 TTAAATATTTATTTTT
1 TTAAATATTTATATTT
* *
925266 ATTAATTATTTATTATAT
1 -TTAAATATTTA-TATTT
925284 TT-AATATTTAT-TTAAT
1 TTAAATATTTATATT--T
925300 ATTAAA-A-TTATATTT
1 -TTAAATATTTATATTT
*
925315 TTAAATATTTATAATT
1 TTAAATATTTATATTT
925331 TTAA
1 TTAA
925335 TTTAATAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 23 0.43
17 17 0.31
18 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATATTTATATTT
Found at i:926911 original size:2 final size:2
Alignment explanation
Indices: 926904--926939 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
926894 AGCCTTAATA
926904 CT CT CT 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 CT CT CT
926940 AGTCTGTCCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:931043 original size:2 final size:2
Alignment explanation
Indices: 931038--931078 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
931028 CACATACATT
931038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
931079 GAATTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:934699 original size:12 final size:12
Alignment explanation
Indices: 934682--934708 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
934672 TCACCATCAT
934682 CTTCTTCTTCTA
1 CTTCTTCTTCTA
934694 CTTCTTCTTCTA
1 CTTCTTCTTCTA
934706 CTT
1 CTT
934709 GTTCCACTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.59
Consensus pattern (12 bp):
CTTCTTCTTCTA
Found at i:935945 original size:17 final size:16
Alignment explanation
Indices: 935916--935951 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
935906 ATTTTTTCAA
935916 CTCTCCTTTTTTTCTC
1 CTCTCCTTTTTTTCTC
*
935932 CTCTCTTTTCTTTTCTC
1 CTCTCCTTT-TTTTCTC
935949 CTC
1 CTC
935952 CTTATCCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTCCTTTTTTTCTC
Found at i:936297 original size:34 final size:33
Alignment explanation
Indices: 936225--936441 Score: 247
Period size: 34 Copynumber: 6.5 Consensus size: 33
936215 CTCTTCCTTC
* * *
936225 TGTTGATTAAATGGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGTAATTTGGTAGCTTACCAT
* * *
936258 TGTTGATTAAATGAGTAATTTGGTGGTTTGCCAT
1 TGTTGATTAAATG-GTAATTTGGTAGCTTACCAT
* *
936292 TGTTGACTAAATGG-AGATTTGGTAGCTTATCAT
1 TGTTGATTAAATGGTA-ATTTGGTAGCTTACCAT
*
936325 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTAATTTGGTAGCTTACCAT
* *
936359 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT-GGTAATTTGGTAGCTTACCAT
* * * *
936393 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGTA-ATTTGGTAGCTTACCAT
936427 TGTTGATTAAATGGT
1 TGTTGATTAAATGGT
936442 GGTTTTTACC
Statistics
Matches: 157, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
32 1 0.01
33 40 0.25
34 115 0.73
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (33 bp):
TGTTGATTAAATGGTAATTTGGTAGCTTACCAT
Found at i:936404 original size:68 final size:67
Alignment explanation
Indices: 936225--936442 Score: 301
Period size: 67 Copynumber: 3.2 Consensus size: 67
936215 CTCTTCCTTC
* * * * * *
936225 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGAGTAATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTGCC
936290 AT
66 AT
* * * *
936292 TGTTGACTAAATGGAGATTTGGTAGCTTATCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTGCC
936357 AT
66 AT
* * * *
936359 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTGC
936424 CAT
65 CAT
936427 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
936443 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTGCC
AT
Found at i:936800 original size:19 final size:19
Alignment explanation
Indices: 936745--936806 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
936735 GGTTGTCGAT
**
936745 GTACTATTCACGTATATAG
1 GTACTATTCACGTATACGG
936764 GTACTATTCACGTATACGG
1 GTACTATTCACGTATACGG
*
936783 GTACTATTCAAGTATACGG
1 GTACTATTCACGTATACGG
*
936802 TTACT
1 GTACT
936807 GTACACGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (19 bp):
GTACTATTCACGTATACGG
Found at i:940941 original size:34 final size:34
Alignment explanation
Indices: 940872--941089 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
940862 AAGTGGGAGA
* * *
940872 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
940905 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
940939 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
940972 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
941006 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
941040 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
941074 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
941090 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:941055 original size:68 final size:67
Alignment explanation
Indices: 940872--941091 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
940862 AAGTGGGAGA
* * * * *
940872 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
940937 CC
66 CC
* * * *
940939 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
941004 CC
66 CC
* * *
941006 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
941071 GCC
65 GCC
941074 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
941092 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:942706 original size:22 final size:22
Alignment explanation
Indices: 942659--942723 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 22
942649 ATTATTCATT
*
942659 TAATAAAAAT-TTAAT-TAAAA
1 TAATATAAATATTAATATAAAA
942679 -ATATATAAATATTAATATAAAA
1 TA-ATATAAATATTAATATAAAA
942701 TAATAT---TATTAATAATAAAA
1 TAATATAAATATTAAT-ATAAAA
942721 TAA
1 TAA
942724 CAAAACTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 8 0.21
20 16 0.41
21 5 0.13
22 9 0.23
23 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATATAAATATTAATATAAAA
Found at i:943086 original size:26 final size:27
Alignment explanation
Indices: 943052--943104 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
943042 AAGCTTTAAA
943052 TTAATATATATATAA-TA-AAAATAAAAT
1 TTAATATAT-TA-AATTATAAAATAAAAT
943079 TTAA-ATATTAAATTATAAAATAAAAT
1 TTAATATATTAAATTATAAAATAAAAT
943105 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.08
25 4 0.17
26 14 0.58
27 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TTAATATATTAAATTATAAAATAAAAT
Found at i:952653 original size:17 final size:17
Alignment explanation
Indices: 952633--952667 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
952623 ATATTTAACA
952633 TAAATATTTTAATATTT
1 TAAATATTTTAATATTT
* *
952650 TAAATTTTTTCATATTT
1 TAAATATTTTAATATTT
952667 T
1 T
952668 GAAGGGTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TAAATATTTTAATATTT
Found at i:954183 original size:2 final size:2
Alignment explanation
Indices: 954178--954222 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
954168 CTCTCTTTCC
*
954178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
954220 AT A
1 AT A
954223 CATGCTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:954377 original size:13 final size:13
Alignment explanation
Indices: 954359--954385 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
954349 GGAAAGATGT
954359 TTTGCATACACTC
1 TTTGCATACACTC
954372 TTTGCATACACTC
1 TTTGCATACACTC
954385 T
1 T
954386 CAGACAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGCATACACTC
Found at i:957532 original size:2 final size:2
Alignment explanation
Indices: 957525--957555 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
957515 GAGCAATAGA
957525 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
957556 AATGTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:958801 original size:2 final size:2
Alignment explanation
Indices: 958794--958831 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
958784 AGGACCCAGA
958794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
958832 TAATATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:959329 original size:15 final size:15
Alignment explanation
Indices: 959309--959338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
959299 TTTAAATTTT
*
959309 TTTAAAAATTAAATA
1 TTTAAAAATAAAATA
959324 TTTAAAAATAAAATA
1 TTTAAAAATAAAATA
959339 ATAATTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAATAAAATA
Found at i:960687 original size:19 final size:21
Alignment explanation
Indices: 960648--960689 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
960638 AAATCTACCC
960648 TTTTAAATATAAATAAGTGAT
1 TTTTAAATATAAATAAGTGAT
*
960669 TTTTAAAT-T-AATAATTGAT
1 TTTTAAATATAAATAAGTGAT
960688 TT
1 TT
960690 AATAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTAAATATAAATAAGTGAT
Found at i:961018 original size:15 final size:16
Alignment explanation
Indices: 960998--961030 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
960988 TTTTTTGAAA
960998 AATGTAT-AATTGTTT
1 AATGTATAAATTGTTT
961013 AATGTATAAATTGTTT
1 AATGTATAAATTGTTT
961029 AA
1 AA
961031 AGAACTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (16 bp):
AATGTATAAATTGTTT
Found at i:962395 original size:97 final size:97
Alignment explanation
Indices: 962251--962476 Score: 317
Period size: 97 Copynumber: 2.3 Consensus size: 97
962241 TTTTTTATTG
* * * *
962251 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCTCCGATGATAACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGAGTTGAAATGTCTCCGATGATAACAATTTA
962316 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
66 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
* * * * * * *
962348 AAAAGCGTGGTTGGAGTATCCCCTCGAAGGAATGGAGTTGAAATGTCTTCGATGGTGATAGTTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGAGTTGAAATGTCTCCGATGATAACAATTTA
* * *
962413 AGTGAGAATAAGATTTAAATTTTGATGTGTTT
66 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
*
962445 AAAAGCGGGGTTGGAGTATCCCTTCGGAGGAA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAA
962477 GAGGGTTGGA
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 112 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (97 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGAGTTGAAATGTCTCCGATGATAACAATTTA
AGTGAGAATAAAATTTAAACTTTGATGCGTTT
Found at i:965477 original size:28 final size:29
Alignment explanation
Indices: 965329--965798 Score: 221
Period size: 28 Copynumber: 15.8 Consensus size: 29
965319 CACATACTTG
* *
965329 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
* * * * *
965357 TGTAGG-TTTGAAAAAAAAGTTGCCACCGATTT
1 TGTGGGCTTTG---AAAATGATGCCACTGA-CT
* **
965389 GTGTGGGTTTTGAAAAT-ATATCACTGACT
1 -TGTGGGCTTTGAAAATGATGCCACTGACT
* * * * *
965418 TGTAGGTTTTGAAAAAGATGCCACTTATT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
* *
965447 TGTGGGTTTTGAAAATG-TGTCACTGACT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
**
965475 TGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAAATG-ATGCCACTGACT
*
965505 TGTGGACTTTG-AAATGATGCCACTGACT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
*
965533 TGTGGGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
* *
965561 TGTGGGCTTTG-AAATGGGTTGCCACCGACT
1 TGTGGGCTTTGAAAAT--GATGCCACTGACT
*
965591 TGAGTGGGCTTTG-AAATGGGTTGCCA-TCGACT
1 T--GTGGGCTTTGAAAAT--GATGCCACT-GACT
* ***
965623 TGAGTGGGCTTTG-AAATGAGTTGTCACCGTTTTT
1 T--GTGGGCTTTGAAAATGA--TGCCA-C-TGACT
* * **
965657 TGTGGGCTTTG-ACATGGGTTGCCACCAACTT
1 TGTGGGCTTTGAAAAT--GATGCCACTGAC-T
* *
965688 GTGTGGGCTTT-CAAATGAGTTGCCACCGACT
1 -TGTGGGCTTTGAAAATGA--TGCCACTGACT
* * * *
965719 TGTGTGCTTTG-AAACGATACCACTGATT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
* ** *
965747 TGTGGGCTTTAAAAAAAATGCTACTGACT
1 TGTGGGCTTTGAAAATGATGCCACTGACT
* *
965776 TGTGAGTTTTG-AAATGATGCCAC
1 TGTGGGCTTTGAAAATGATGCCAC
965799 AAAGTTGTGG
Statistics
Matches: 342, Mismatches: 69, Indels: 62
0.72 0.15 0.13
Matches are distributed among these distances:
27 4 0.01
28 117 0.34
29 47 0.14
30 54 0.16
31 19 0.06
32 88 0.26
33 5 0.01
34 7 0.02
35 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (29 bp):
TGTGGGCTTTGAAAATGATGCCACTGACT
Found at i:965529 original size:58 final size:57
Alignment explanation
Indices: 965297--965854 Score: 261
Period size: 57 Copynumber: 9.4 Consensus size: 57
965287 CACTAACTTA
* * * *
965297 TGTGGGCTTTGAAAAGAGTTGTCACAT-ACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GATGCCAC-TGAC-T-TGTGGGCTTTGAAATGATGCCACTGACT
* * * * * * **
965357 TGTAGG-TTTGAAAAAAAAGTTGCCACCGATTTGTGTGGGTTTTGAAAAT-ATATCACTGACT
1 TGTGGGCTTTG---AAAAGGATGCCACTGA-CT-TGTGGGCTTTG-AAATGATGCCACTGACT
* * * * * * *
965418 TGTAGGTTTTGAAAAAGATGCCACTTATTTGTGGGTTTTGAAAATG-TGTCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTG-AAATGATGCCACTGACT
* *
965475 TGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGACTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-ATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGACT
* *
965533 TGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAT--GATGCCACTGACT
* * * **
965591 TGAGTGGGCTTTGAAATGGGTTGCCA-TCGACTTGAGTGGGCTTTGAAATGAGTTGTCACCGTTT
1 T--GTGGGCTTTGAAA-AGGATGCCACT-GACTT--GTGGGCTTTGAAATGA--TGCCA-C-TGA
*
965655 TT
56 CT
** * ** * *
965657 TGTGGGCTTTGACATGGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACCGACT
1 TGTGGGCTTTGA-AAAGGATGCCACTGAC-T-TGTGGGCTTTGAAATGA--TGCCACTGACT
* * * * * ** *
965719 TGTGTGCTTTG-AAACGATACCACTGATTTGTGGGCTTTAAAAAAAATGCTACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTT-GAAATGATGCCACTGACT
* * * ** * * * * * * *
965776 TGTGAGTTTTG-AAATGATGCCACAAAGTTGTGGGTTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGACT
* *
965832 TGTGAGCTTT-AAAAGGGTGCCAC
1 TGTGGGCTTTGAAAAGGATGCCAC
965855 GGAGCTATGG
Statistics
Matches: 394, Mismatches: 75, Indels: 62
0.74 0.14 0.12
Matches are distributed among these distances:
56 57 0.14
57 88 0.22
58 63 0.16
59 22 0.06
60 22 0.06
61 39 0.10
62 35 0.09
63 1 0.00
64 61 0.15
65 3 0.01
66 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGACT
Found at i:965603 original size:32 final size:30
Alignment explanation
Indices: 965471--965732 Score: 255
Period size: 32 Copynumber: 8.6 Consensus size: 30
965461 ATGTGTCACT
*
965471 GACTTGTGGGCTTTGAAA-GGGTATGCCACT
1 GACTTGTGGGCTTTGAAATGGGT-TGCCACC
* * *
965501 GACTTGTGGACTTTGAAAT--GATGCCACT
1 GACTTGTGGGCTTTGAAATGGGTTGCCACC
* * *
965529 GACTTGTGGGCTTT-AAA-AGGATGCCACT
1 GACTTGTGGGCTTTGAAATGGGTTGCCACC
965557 GACTTGTGGGCTTTGAAATGGGTTGCCACC
1 GACTTGTGGGCTTTGAAATGGGTTGCCACC
*
965587 GACTTGAGTGGGCTTTGAAATGGGTTGCCATC
1 GACTT--GTGGGCTTTGAAATGGGTTGCCACC
* *
965619 GACTTGAGTGGGCTTTGAAATGAGTTGTCACC
1 GACTT--GTGGGCTTTGAAATGGGTTGCCACC
** *
965651 GTTTTTTGTGGGCTTTGACATGGGTTGCCACC
1 G--ACTTGTGGGCTTTGAAATGGGTTGCCACC
* * *
965683 AACTTGTGTGGGCTTTCAAATGAGTTGCCACC
1 GAC-T-TGTGGGCTTTGAAATGGGTTGCCACC
*
965715 GACTTGTGTGCTTTGAAA
1 GACTTGTGGGCTTTGAAA
965733 CGATACCACT
Statistics
Matches: 197, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
27 3 0.02
28 43 0.22
29 4 0.02
30 42 0.21
31 2 0.01
32 101 0.51
34 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (30 bp):
GACTTGTGGGCTTTGAAATGGGTTGCCACC
Found at i:965806 original size:28 final size:28
Alignment explanation
Indices: 965775--965854 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
965765 TGCTACTGAC
* *
965775 TTGTGAGTTTTGAAATGATGCCACAAAG
1 TTGTGAGTTTTAAAAGGATGCCACAAAG
* * **
965803 TTGTGGGTTTTAAAAGGGTGCCACGGAG
1 TTGTGAGTTTTAAAAGGATGCCACAAAG
* *
965831 TTGTGAGCTTTAAAAGGGTGCCAC
1 TTGTGAGTTTTAAAAGGATGCCAC
965855 GGAGCTATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.30
Consensus pattern (28 bp):
TTGTGAGTTTTAAAAGGATGCCACAAAG
Found at i:965855 original size:28 final size:28
Alignment explanation
Indices: 965801--966479 Score: 668
Period size: 28 Copynumber: 24.6 Consensus size: 28
965791 GATGCCACAA
**
965801 AGTTGTGGGTTTTAAAAGGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
965829 AGTTGT-GAGCTTTAAAAGGGTGCCACGG
1 AGTTGTGGA-CTTTAAAAGGGTGCCACGG
* * * * *
965857 AGCTATGGATTTTAAAAAGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
965885 AGTTGTGAACTTTAAAAGGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
965913 AGTTGTGGACTAT-AAAGGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* * * *
965940 AATTGCGGAC-TT-AAAGGGTTGCAACAG
1 AGTTGTGGACTTTAAAAGGG-TGCCACGG
* *
965967 AGTTGTGGACTTTAAAAAGTTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
965995 AGTTGTGGACTTT-AAAGGTTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
966022 AGTTGTGGACTATAAAAGGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
** * *
966050 AGTTGTGGACTTTAAAAGATTACTACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* * *
966078 AGCTGTGGAC-TTAAAAGTGTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966105 AGTTGTGGAC-TTAAAAGTGTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966132 AGTTGTGGACTTAAAAAGGGTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
966160 AGTTGT-GAGTTTTAAAAGGGTGCCACGG
1 AGTTGTGGA-CTTTAAAAGGGTGCCACGG
** * *
966188 AACTGTGGACTTTAAAAAGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966216 AGTTGTGAACTTTAAAAGGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966244 AGTTGTGGACTAT-AAAGGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* * * **
966271 AATTGCGGAC-TT-AAAGGGTTGCAATAG
1 AGTTGTGGACTTTAAAAGGG-TGCCACGG
* * * *
966298 AGTTGTGGATTTTAAAAAGTTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966326 AGTTGTGGACTTT-AAAGGTTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* *
966353 AGTTGTGGACTATAAAAGGGTGTCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
** * *
966381 AGTTGTGGACTTTAAAAGATTGCTATGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
* * *
966409 AGCTGTGGA-TTTAAAAGTGTGCCACAG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
*
966436 AGTTGTGGAC-TTAAAAGTGTGCCACGG
1 AGTTGTGGACTTTAAAAGGGTGCCACGG
966463 AGTTGTGGAC-TTAAAAG
1 AGTTGTGGACTTTAAAAG
966480 AAATACCACG
Statistics
Matches: 540, Mismatches: 97, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
26 14 0.03
27 220 0.41
28 294 0.54
29 12 0.02
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (28 bp):
AGTTGTGGACTTTAAAAGGGTGCCACGG
Found at i:966395 original size:331 final size:331
Alignment explanation
Indices: 965793--966478 Score: 1219
Period size: 331 Copynumber: 2.1 Consensus size: 331
965783 TTTGAAATGA
* ** * *
965793 TGCCACAAAGTTGTGGGTTTTAAAAGGGTGCCACGGAGTTGTGAGCTTTAAAAGGGTGCCACGGA
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGTTGTGAGCTTTAAAAGGGTGCCACGGA
* *
965858 GCTATGGATTTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
66 ACTATGGACTTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
965923 TATAAAGGGTGTCACGGAATTGCGGACTTAAAGGGTTGCAACAGAGTTGTGGACTTTAAAAAGTT
131 TATAAAGGGTGTCACGGAATTGCGGACTTAAAGGGTTGCAACAGAGTTGTGGACTTTAAAAAGTT
965988 GCCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGACTATAAAAGGGTGCCACGGAGT
196 GCCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGACTATAAAAGGGTGCCACGGAGT
966053 TGTGGACTTTAAAAGATTACTACGGAGCTGTGGACTTAAAAGTGTGCCACAGAGTTGTGGACTTA
261 TGTGGACTTTAAAAGATTACTACGGAGCTGTGGACTTAAAAGTGTGCCACAGAGTTGTGGACTTA
966118 AAAGTG
326 AAAGTG
*
966124 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGTTGTGAGTTTTAAAAGGGTGCCACGGA
1 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGTTGTGAGCTTTAAAAGGGTGCCACGGA
*
966189 ACTGTGGACTTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
66 ACTATGGACTTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
* *
966254 TATAAAGGGTGTCACGGAATTGCGGACTTAAAGGGTTGCAATAGAGTTGTGGATTTTAAAAAGTT
131 TATAAAGGGTGTCACGGAATTGCGGACTTAAAGGGTTGCAACAGAGTTGTGGACTTTAAAAAGTT
* *
966319 GTCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGACTATAAAAGGGTGTCACGGAGT
196 GCCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGACTATAAAAGGGTGCCACGGAGT
* * *
966384 TGTGGACTTTAAAAGATTGCTATGGAGCTGTGGATTTAAAAGTGTGCCACAGAGTTGTGGACTTA
261 TGTGGACTTTAAAAGATTACTACGGAGCTGTGGACTTAAAAGTGTGCCACAGAGTTGTGGACTTA
966449 AAAGTG
326 AAAGTG
*
966455 TGCCACGGAGTTGTGGACTTAAAA
1 TGCCACAGAGTTGTGGACTTAAAA
966479 GAAATACCAC
Statistics
Matches: 338, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
331 338 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (331 bp):
TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGTTGTGAGCTTTAAAAGGGTGCCACGGA
ACTATGGACTTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
TATAAAGGGTGTCACGGAATTGCGGACTTAAAGGGTTGCAACAGAGTTGTGGACTTTAAAAAGTT
GCCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGACTATAAAAGGGTGCCACGGAGT
TGTGGACTTTAAAAGATTACTACGGAGCTGTGGACTTAAAAGTGTGCCACAGAGTTGTGGACTTA
AAAGTG
Found at i:966491 original size:110 final size:110
Alignment explanation
Indices: 965793--966479 Score: 709
Period size: 110 Copynumber: 6.2 Consensus size: 110
965783 TTTGAAATGA
* ** * *
965793 TGCCACAAAGTTGTGGGTTTTAAAAGGGTGCCACGGAGTTGT-GAGCTTTAAAAGGGTGCCACGG
1 TGCCACAGAGTTGT-GGACTTAAAAGGGTGCCACGGAGTTGTGGA-CTTTAAAAGGTTGCAACGG
* * * *
965857 AGCTATGGATTTTAAAAAG-GTGTCACGGAGTTGTGAACTTTAAAAGGG
64 AGCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGAC-TTAAAA-GG
* * * * * * *
965905 TGTCACGGAGTTGTGGAC-TATAAAGGGTGTCACGGAATTGCGGAC-TTAAAGGGTTGCAACAGA
1 TGCCACAGAGTTGTGGACTTA-AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTTGCAACGGA
* *
965968 GTTGTGGACTTTAAAAAGT-TGCCACGGAGTTGTGGACTTTAAAGG
65 GCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
966013 TTGCCACAGAGTTGTGGACTATAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGATTACTACGG
1 -TGCCACAGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTTGCAACGG
*
966078 AGCTGTGGAC-TT-AAAAGTGTGCCACAGAGTTGTGGACTTAAAAGTG
64 AGCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGACTTAAAAG-G
* * * *
966124 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGTTGT-GAGTTTTAAAAGGGTGCCACGG
1 TGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGA-CTTTAAAAGGTTGCAACGG
* * *
966188 AACTGTGGACTTTAAAAAG-GTGTCACGGAGTTGTGAACTTTAAAAGGG
64 AGCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGAC-TTAAAA-GG
* * * * * * **
966236 TGTCACGGAGTTGTGGAC-TATAAAGGGTGTCACGGAATTGCGGAC-TTAAAGGGTTGCAATAGA
1 TGCCACAGAGTTGTGGACTTA-AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTTGCAACGGA
* * * *
966299 GTTGTGGATTTTAAAAAGT-TGTCACGGAGTTGTGGACTTTAAAGG
65 GCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGACTTAAAAGG
* * * *
966344 TTGCCACAGAGTTGTGGACTATAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGATTGCTATGG
1 -TGCCACAGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTTGCAACGG
*
966409 AGCTGTGGA-TTT-AAAAGTGTGCCACAGAGTTGTGGACTTAAAAGTG
64 AGCTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGACTTAAAAG-G
*
966455 TGCCACGGAGTTGTGGACTTAAAAG
1 TGCCACAGAGTTGTGGACTTAAAAG
966480 AAATACCACG
Statistics
Matches: 480, Mismatches: 71, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
108 4 0.01
109 63 0.13
110 266 0.55
111 103 0.21
112 43 0.09
113 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (110 bp):
TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTTGCAACGGAG
CTGTGGACTTTAAAAAGTGTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:966498 original size:28 final size:27
Alignment explanation
Indices: 966440--966501 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
966430 CCACAGAGTT
** * * *
966440 GTGGACTTAAAAGTGTGCCACGGAGTT
1 GTGGACTTAAAAGAATACCACGGAATC
966467 GTGGACTTAAAAGAAATACCACGGAATC
1 GTGGACTTAAAAG-AATACCACGGAATC
966495 GTGGACT
1 GTGGACT
966502 CTGAAGAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (27 bp):
GTGGACTTAAAAGAATACCACGGAATC
Found at i:966501 original size:55 final size:54
Alignment explanation
Indices: 965812--966479 Score: 617
Period size: 55 Copynumber: 12.1 Consensus size: 54
965802 GTTGTGGGTT
* * *
965812 TTAAAAGGGTGCCACGGAGTTGT-GAGCTTTAAAAGGGTGCCACGGAGCTATGGATT
1 TTAAAAGGGTGCCACGGAGTTGTGGA-C-TTAAAAGGGTGCCACGGAGTTGTGGA-C
* * * *
965868 TTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
* * * * *
965923 -TATAAAGGGTGTCACGGAATTGCGGACTT-AAAGGGTTGCAACAGAGTTGTGGAC
1 TTA-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGAC
* * * * *
965977 TTTAAAAAGTTGCCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
** * * *
966032 TATAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGATTACTACGGAGCTGTGGAC
1 T-TAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
966088 TTAAAAGTGTGCCACAGAGTTGTGGACTTAAAAGTGTGCCACAGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* ** **
966142 TTAAAAAGGGTGCCACAGAGTTGTGAGTTTTAAAAGGGTGCCACGGAACTGTGGAC
1 TT-AAAAGGGTGCCACGGAGTTGTG-GACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * * *
966198 TTTAAAAAGGTGTCACGGAGTTGTGAACTTTAAAAGGGTGTCACGGAGTTGTGGAC
1 -TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
* * * * ** *
966254 -TATAAAGGGTGTCACGGAATTGCGGACTT-AAAGGGTTGCAATAGAGTTGTGGATT
1 TTA-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGA-C
* * * * * *
966309 TTAAAAAGTTGTCACGGAGTTGTGGACTTTAAAGGTTGCCACAGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* ** * * * *
966363 TATAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGATTGCTATGGAGCTGTGGAT
1 T-TAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
966419 TTAAAAGTGTGCCACAGAGTTGTGGACTTAAAAGTGTGCCACGGAGTTGTGGAC
1 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
966473 TTAAAAG
1 TTAAAAG
966480 AAATACCACG
Statistics
Matches: 505, Mismatches: 88, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
53 12 0.02
54 89 0.18
55 231 0.46
56 170 0.34
57 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (54 bp):
TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
Found at i:971507 original size:98 final size:98
Alignment explanation
Indices: 971377--971624 Score: 319
Period size: 98 Copynumber: 2.6 Consensus size: 98
971367 AATTTTATTT
*
971377 ATCGGGGA-TACTTCAACCCTATTCCTCCGAGGGGATACTCCAACC-CTGTTTTTAAACACATCA
1 ATCGGGGACTACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCTC-GCTTTTAAACACATCA
971440 AAATTTAAATCTTATTCTCACTTAAATTATCA-C
65 AAATTTAAATCTTATTCTCACTTAAATTATCATC
* * * *
971473 AATCGGGGACTATTTCAACCCTATTTCTCCGAGGGGATATTCCAACCTCGCTTTTAAACGCATCA
1 -ATCGGGGACTACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGCTTTTAAACACATCA
* * * *
971538 AAGTTTAAATTTTATTCTCACTTAAGTTGTCATC
65 AAATTTAAATCTTATTCTCACTTAAATTATCATC
* *
971572 ATCGGGGAC-ACCTT-AACTCC-ATTCCTCCGAGGGGATACTCCAATCTCGTTTTT
1 ATCGGGGACTA-CTTCAAC-CCTATTCCTCCGAGGGGATACTCCAACCTCGCTTTT
971625 CAATCAAAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
97 41 0.31
98 89 0.67
99 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (98 bp):
ATCGGGGACTACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGCTTTTAAACACATCAA
AATTTAAATCTTATTCTCACTTAAATTATCATC
Found at i:973334 original size:11 final size:11
Alignment explanation
Indices: 973318--973343 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
973308 ATTTTGCTGA
973318 TGAATGCAAAG
1 TGAATGCAAAG
973329 TGAATGCAAAG
1 TGAATGCAAAG
973340 TGAA
1 TGAA
973344 ATTAATGTAT
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:0.46, C:0.08, G:0.27, T:0.19
Consensus pattern (11 bp):
TGAATGCAAAG
Found at i:976826 original size:22 final size:21
Alignment explanation
Indices: 976800--976858 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
976790 ATGATACAAT
*
976800 ATTTTAATTTTTTTAATCTCTA
1 ATTTTAATTTTTTTAATAT-TA
976822 ATTTT--TTATTTTTAA-ATTA
1 ATTTTAATT-TTTTTAATATTA
976841 ATTATTAATTTTTTTAAT
1 ATT-TTAATTTTTTTAAT
976859 TAATTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 14 0.45
22 7 0.23
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTAATTTTTTTAATATTA
Found at i:976859 original size:16 final size:17
Alignment explanation
Indices: 976838--976871 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
976828 TATTTTTAAA
976838 TTAATT-ATTAATTTTT
1 TTAATTAATTAATTTTT
*
976854 TTAATTAATTTATTTTT
1 TTAATTAATTAATTTTT
976871 T
1 T
976872 AAAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTAATTAATTAATTTTT
Found at i:976859 original size:20 final size:20
Alignment explanation
Indices: 976803--976863 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
976793 ATACAATATT
*
976803 TTAATTTTTTTAATCTCTAATTT
1 TTAATTTTTTTAA--T-TAATTA
* *
976826 TTTA-TTTTTAAATTAATTA
1 TTAATTTTTTTAATTAATTA
976845 TTAATTTTTTTAATTAATT
1 TTAATTTTTTTAATTAATT
976864 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.25
20 14 0.44
22 7 0.22
23 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAATTTTTTTAATTAATTA
Found at i:976872 original size:16 final size:17
Alignment explanation
Indices: 976825--976873 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
976815 ATCTCTAATT
*
976825 TTTTATTTTTAAATTAA
1 TTTTATTTTTTAATTAA
976842 TTATTAATTTTTTTAATTAA
1 TT-TT-A-TTTTTTAATTAA
976862 -TTTATTTTTTAA
1 TTTTATTTTTTAA
976874 AATTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.29
17 3 0.11
18 4 0.14
19 2 0.07
20 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTTTTTAATTAA
Found at i:984633 original size:29 final size:30
Alignment explanation
Indices: 984577--984639 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
984567 ACCAAAGTAT
* * *
984577 TGTTAATTTTTAAATAAATTATTAAAATAA
1 TGTTAATTTTGAAACAAATTACTAAAATAA
* *
984607 TGTTAA-TTTGAAACAAATTACTGAAATAC
1 TGTTAATTTTGAAACAAATTACTAAAATAA
984636 TGTT
1 TGTT
984640 GTTTTGACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (30 bp):
TGTTAATTTTGAAACAAATTACTAAAATAA
Found at i:984832 original size:39 final size:40
Alignment explanation
Indices: 984774--984849 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
984764 CCTACTGTTA
*
984774 TTATTATAATGTTAATATTT-TTGAATAATATTATTAGGG
1 TTATTATAATGTTAATATTTCTTCAATAATATTATTAGGG
* ** *
984813 TTATTATTATGTTCGTATTTCTTCAATTATATTATTA
1 TTATTATAATGTTAATATTTCTTCAATAATATTATTA
984850 TGTTGGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 17 0.55
40 14 0.45
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (40 bp):
TTATTATAATGTTAATATTTCTTCAATAATATTATTAGGG
Found at i:984845 original size:28 final size:28
Alignment explanation
Indices: 984814--984869 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
984804 TTATTAGGGT
*
984814 TATTATTATGTTCGTATTTCTTCAATTA
1 TATTATTATGTTCGTATTTCTTAAATTA
* *
984842 TATTATTATGTTGGTATTTTTTAAATTA
1 TATTATTATGTTCGTATTTCTTAAATTA
984870 ATAAAAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (28 bp):
TATTATTATGTTCGTATTTCTTAAATTA
Found at i:984890 original size:19 final size:19
Alignment explanation
Indices: 984866--984911 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
984856 TATTTTTTAA
*
984866 ATTAATAAAAGATTATATT
1 ATTAATAAAAGATAATATT
984885 ATTAATAAAAGATAATATT
1 ATTAATAAAAGATAATATT
984904 ATT-ATAAA
1 ATTAATAAA
984912 TATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
ATTAATAAAAGATAATATT
Found at i:985110 original size:31 final size:31
Alignment explanation
Indices: 985075--985197 Score: 102
Period size: 31 Copynumber: 4.2 Consensus size: 31
985065 ACTTTTTAAA
985075 TTTAAATTAAGAGTTGTAATTGTCTAATTAT
1 TTTAAATTAAGAGTTGTAATTGTCTAATTAT
985106 TTTAAAATTTAA-A-TTGTAATTGTCT-A--A-
1 TTT-AAA-TTAAGAGTTGTAATTGTCTAATTAT
* * * **
985133 -TT--ATTAAGGGTTGCAGTCATCTAATTAT
1 TTTAAATTAAGAGTTGTAATTGTCTAATTAT
* *
985161 TTTAAATTAAGGGTTGTACTTGTCTAATTAT
1 TTTAAATTAAGAGTTGTAATTGTCTAATTAT
985192 TTTAAA
1 TTTAAA
985198 ATTTTAATTC
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
22 4 0.06
23 1 0.01
24 8 0.11
25 1 0.01
26 2 0.03
27 1 0.01
28 1 0.01
29 2 0.03
30 1 0.01
31 43 0.60
32 4 0.06
33 4 0.06
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (31 bp):
TTTAAATTAAGAGTTGTAATTGTCTAATTAT
Found at i:985271 original size:17 final size:17
Alignment explanation
Indices: 985223--985277 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 17
985213 GGTTGTAATT
985223 TTTTAATTATTTTTAAAA
1 TTTTAATTA-TTTTAAAA
985241 TTAATTATAGTTATTTTAAAA
1 TT--TTA-A-TTATTTTAAAA
985262 TTTTAATTATTTTAAA
1 TTTTAATTATTTTAAA
985278 TTGCTAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 10 0.30
18 3 0.09
19 3 0.09
20 3 0.09
21 11 0.33
22 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTTAATTATTTTAAAA
Found at i:990110 original size:53 final size:53
Alignment explanation
Indices: 990032--990138 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
990022 TCACATAGTT
*
990032 TATGGTGACCTTTTTTTATCGCTTAAAAAATGAGTTCTCTAGCTGCTAACATA
1 TATGGTGACCTTTTTTTATCACTTAAAAAATGAGTTCTCTAGCTGCTAACATA
990085 TATGGTGA-CTTCTTTTTATCACTTAAAAAATGAGTTCTCTAGCTGCTAACATA
1 TATGGTGACCTT-TTTTTATCACTTAAAAAATGAGTTCTCTAGCTGCTAACATA
990138 T
1 T
990139 TTCTTTAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
52 3 0.06
53 49 0.94
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (53 bp):
TATGGTGACCTTTTTTTATCACTTAAAAAATGAGTTCTCTAGCTGCTAACATA
Found at i:997777 original size:14 final size:16
Alignment explanation
Indices: 997757--997805 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
997747 ATTTATATAC
*
997757 AATATATAAT-ATTTT
1 AATATATAATAATTAT
997772 AA-ATATAATAATTAT
1 AATATATAATAATTAT
*
997787 AATATATAAAAATATAT
1 AATATATAATAAT-TAT
997804 AA
1 AA
997806 AAATGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.24
15 8 0.28
16 9 0.31
17 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATAATAATTAT
Found at i:998253 original size:38 final size:38
Alignment explanation
Indices: 998179--998253 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
998169 GCCGACGCTA
* * **
998179 AGGGTGTGTTTGATAAATTGAAAAAGTTAACTGATGAG
1 AGGGTGTGTTTAATAAATTGAAAAAGTGAAAGGATGAG
* *
998217 AGGGTGTGTTTAATACATTTAAAAAGTGAAAGGATGA
1 AGGGTGTGTTTAATAAATTGAAAAAGTGAAAGGATGA
998254 AAAGAAGAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.31
Consensus pattern (38 bp):
AGGGTGTGTTTAATAAATTGAAAAAGTGAAAGGATGAG
Found at i:998719 original size:16 final size:16
Alignment explanation
Indices: 998679--998724 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
998669 GATCGATTTA
*
998679 AATTCGAAAATAGTTCG
1 AATTC-AAAATAATTCG
**
998696 AACCCAAAATAATTCG
1 AATTCAAAATAATTCG
998712 AATTCAAAATAAT
1 AATTCAAAATAAT
998725 ATAAACTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTCAAAATAATTCG
Found at i:999635 original size:16 final size:17
Alignment explanation
Indices: 999587--999635 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
999577 TTGACTCGTA
999587 TTCAAAATGATTCGAA-
1 TTCAAAATGATTCGAAC
*
999603 TTCAAAATAATTCGAAC
1 TTCAAAATGATTCGAAC
*
999620 TT-AAAATGACTCGAAC
1 TTCAAAATGATTCGAAC
999636 CCAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (17 bp):
TTCAAAATGATTCGAAC
Found at i:999641 original size:16 final size:16
Alignment explanation
Indices: 999588--999642 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
999578 TGACTCGTAT
*
999588 TCAAAATGATTCGAAT
1 TCAAAATGATTCGAAC
*
999604 TCAAAATAATTCGAAC
1 TCAAAATGATTCGAAC
* *
999620 TTAAAATGACTCGAAC
1 TCAAAATGATTCGAAC
*
999636 CCAAAAT
1 TCAAAAT
999643 AATATAAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.25
Consensus pattern (16 bp):
TCAAAATGATTCGAAC
Found at i:1002180 original size:2 final size:2
Alignment explanation
Indices: 1002173--1002203 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1002163 TCCAAAGTCT
1002173 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1002204 TTACCTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1003338 original size:14 final size:15
Alignment explanation
Indices: 1003312--1003342 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1003302 ATTTATTTAC
1003312 ATAAATTTATAATAT
1 ATAAATTTATAATAT
1003327 ATAAATTT-TAATAT
1 ATAAATTTATAATAT
1003341 AT
1 AT
1003343 TTATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAATTTATAATAT
Found at i:1006716 original size:22 final size:22
Alignment explanation
Indices: 1006691--1006744 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1006681 AAATAAACTA
1006691 TATATATTTATT-AATTAATAAT
1 TATATATTTATTGAATTAAT-AT
*
1006713 TATATA-TTATTGATTTAATAT
1 TATATATTTATTGAATTAATAT
1006734 TATAATATTTA
1 TAT-ATATTTA
1006745 AATTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 10 0.36
22 15 0.54
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATATATTTATTGAATTAATAT
Found at i:1011339 original size:21 final size:21
Alignment explanation
Indices: 1011315--1011359 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1011305 GAATAGAATT
1011315 ATTAATTATTAAAAAA-TATAA
1 ATTAATT-TTAAAAAAGTATAA
*
1011336 ATTAATTTTAAAAAAGTTTAA
1 ATTAATTTTAAAAAAGTATAA
1011357 ATT
1 ATT
1011360 GTCTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTAATTTTAAAAAAGTATAA
Found at i:1013329 original size:15 final size:14
Alignment explanation
Indices: 1013309--1013342 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
1013299 TTTCATCACC
1013309 TAAAAAAATATTTTT
1 TAAAAAAATA-TTTT
1013324 TAAAAAAATATTTT
1 TAAAAAAATATTTT
1013338 TAAAA
1 TAAAA
1013343 GTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAAAATATTTT
Found at i:1014047 original size:2 final size:2
Alignment explanation
Indices: 1014040--1014069 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1014030 TGTTGTTTAC
1014040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1014070 GATCAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1014248 original size:2 final size:2
Alignment explanation
Indices: 1014241--1014273 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1014231 AACTTAAAGT
1014241 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 T
1014274 GGAAGAAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1014778 original size:19 final size:20
Alignment explanation
Indices: 1014754--1014793 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1014744 TAACTTGAAA
1014754 TAATAT-TTTTTAATTAAAT
1 TAATATATTTTTAATTAAAT
*
1014773 TAATATATTTTTATTTAAAT
1 TAATATATTTTTAATTAAAT
1014793 T
1 T
1014794 TAATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATATATTTTTAATTAAAT
Found at i:1015514 original size:24 final size:24
Alignment explanation
Indices: 1015480--1015526 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1015470 TTATATATAT
*
1015480 ATATATGTTTAAATATTAAATTTG
1 ATATATCTTTAAATATTAAATTTG
* *
1015504 ATATATCTTTAAATTTTTAATTT
1 ATATATCTTTAAATATTAAATTT
1015527 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
ATATATCTTTAAATATTAAATTTG
Found at i:1018804 original size:27 final size:26
Alignment explanation
Indices: 1018736--1018813 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 26
1018726 ATTTTTAAGT
* * *
1018736 TAATAAAATTAAAATTAAATT-ATTA
1 TAATAAAAATAAAAATAAATTAAATA
1018761 TAA-AAGAATATATAAAATAAATTAAGATA
1 TAATAA-AA-ATA-AAAATAAATTAA-ATA
1018790 TAATAAAAATAAAAA-ATAATTAAA
1 TAATAAAAATAAAAATA-AATTAAA
1018814 ATATGATACG
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
24 2 0.05
25 5 0.12
26 4 0.09
27 19 0.44
28 4 0.09
29 7 0.16
30 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (26 bp):
TAATAAAAATAAAAATAAATTAAATA
Found at i:1019578 original size:2 final size:2
Alignment explanation
Indices: 1019571--1019618 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1019561 CCTTGTTTTG
*
1019571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1019613 AT AT AT
1 AT AT AT
1019619 GCTTTCATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1022397 original size:14 final size:13
Alignment explanation
Indices: 1022361--1022410 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
1022351 AATGTTAATA
*
1022361 ATTAAATTTTATT
1 ATTAAAATTTATT
*
1022374 ATT--TATTTATT
1 ATTAAAATTTATT
1022385 ATTAAAATATTATT
1 ATTAAAAT-TTATT
*
1022399 ATTTAAATTTAT
1 ATTAAAATTTAT
1022411 ATTTAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 9 0.30
13 9 0.30
14 12 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTAAAATTTATT
Found at i:1022451 original size:16 final size:17
Alignment explanation
Indices: 1022430--1022472 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1022420 AAAAAATAAT
1022430 ATTTATTAAATAT-CAA
1 ATTTATTAAATATGCAA
*
1022446 ATTTATTAAATATGTAA
1 ATTTATTAAATATGCAA
1022463 A-TTATTAAAT
1 ATTTATTAAAT
1022473 CAATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTTATTAAATATGCAA
Found at i:1022518 original size:16 final size:16
Alignment explanation
Indices: 1022494--1022538 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1022484 ATAAAATAAA
*
1022494 ATATAAAATTAAATAT
1 ATATTAAATTAAATAT
*
1022510 ATATTAAATTTAATAT
1 ATATTAAATTAAATAT
*
1022526 ATA-TAAAATAAAT
1 ATATTAAATTAAAT
1022539 TAAAATATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTAAATTAAATAT
Found at i:1029656 original size:19 final size:19
Alignment explanation
Indices: 1029632--1029670 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1029622 TGCTGAGAAA
1029632 TTTATTTAAAACAGAACAC
1 TTTATTTAAAACAGAACAC
1029651 TTTATTTAAAACAGAACAC
1 TTTATTTAAAACAGAACAC
1029670 T
1 T
1029671 GGATTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (19 bp):
TTTATTTAAAACAGAACAC
Found at i:1029680 original size:19 final size:19
Alignment explanation
Indices: 1029639--1029680 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1029629 AAATTTATTT
** *
1029639 AAAACAGAACACTTTATTT
1 AAAACAGAACACTGGATTC
1029658 AAAACAGAACACTGGATTC
1 AAAACAGAACACTGGATTC
1029677 AAAA
1 AAAA
1029681 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (19 bp):
AAAACAGAACACTGGATTC
Found at i:1030786 original size:22 final size:23
Alignment explanation
Indices: 1030761--1030812 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
1030751 TAACATATTA
*
1030761 TATATTTATAT-AAATTTTAATT
1 TATAATTATATAAAATTTTAATT
1030783 TATAATTATATAAAATTTTAA--
1 TATAATTATATAAAATTTTAATT
1030804 TATAATTAT
1 TATAATTAT
1030813 TTTTTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.32
22 10 0.36
23 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATAATTATATAAAATTTTAATT
Found at i:1031218 original size:33 final size:30
Alignment explanation
Indices: 1031141--1031226 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
1031131 ATTTTTTAAA
*
1031141 TTTGT-AATTTATAATATAAAAATAGATAT
1 TTTGTAAATTTTTAATATAAAAATAGATAT
*
1031170 TTTATAAAATTTTTAATATAAAAATAGGTATTAT
1 TTTGT-AAATTTTTAATATAAAAATA-G-A-TAT
*
1031204 TTTGTAAATTTTTAAAATAAAAA
1 TTTGTAAATTTTTAATATAAAAA
1031227 ATTTGTTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.08
31 18 0.38
32 1 0.02
33 18 0.38
34 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTGTAAATTTTTAATATAAAAATAGATAT
Found at i:1032464 original size:14 final size:14
Alignment explanation
Indices: 1032447--1032499 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1032437 AATTAAAATA
1032447 TTATTATAATTATT
1 TTATTATAATTATT
*
1032461 TTATTTTAATT-TT
1 TTATTATAATTATT
**
1032474 TATAGAATAATTATT
1 T-TATTATAATTATT
*
1032489 TTAATATAATT
1 TTATTATAATT
1032500 TTATTTTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 3 0.10
14 25 0.81
15 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATTATAATTATT
Found at i:1033030 original size:15 final size:15
Alignment explanation
Indices: 1032986--1033031 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1032976 TATTATTATC
*
1032986 AAAATAAAAATTAAT
1 AAAATAAATATTAAT
1033001 -AAAT-AAT-TT-AT
1 AAAATAAATATTAAT
1033012 AAAATAAATATTAAT
1 AAAATAAATATTAAT
1033027 AAAAT
1 AAAAT
1033032 TTATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
11 2 0.08
12 6 0.23
13 5 0.19
14 6 0.23
15 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAAATATTAAT
Found at i:1033279 original size:9 final size:8
Alignment explanation
Indices: 1033190--1033279 Score: 64
Period size: 8 Copynumber: 11.1 Consensus size: 8
1033180 TTATATTTAA
1033190 AATA-TTT
1 AATATTTT
1033197 AATATTTT
1 AATATTTT
*
1033205 TATAATTTT
1 AAT-ATTTT
*
1033214 AATATATT
1 AATATTTT
1033222 AATATTTAT
1 AATATTT-T
*
1033231 AATA-TAT
1 AATATTTT
1033238 AA-ATTTT
1 AATATTTT
1033245 AA-ATTTT
1 AATATTTT
1033252 -ATATTTATAT
1 AATA-TT-T-T
1033262 AATATTTT
1 AATATTTT
1033270 AATAATTTT
1 AAT-ATTTT
1033279 A
1 A
1033280 TATACATCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
6 2 0.03
7 17 0.25
8 22 0.33
9 20 0.30
10 3 0.04
11 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
AATATTTT
Found at i:1033300 original size:56 final size:55
Alignment explanation
Indices: 1033180--1033307 Score: 125
Period size: 56 Copynumber: 2.3 Consensus size: 55
1033170 TACGTTAAGA
* * **
1033180 TTATATTTAAAATATTTAATATTTTTATAATTTTAATATATTAATATTTATAATAT
1 TTATATTTTAAAT-TTTAATATTTATATAATTTTAATATATTAATATACATAATAT
* * * *
1033236 ATAAATTTTAAATTTT-ATATTTATATAATATTTTAATA-ATTTTATATACATCATAT
1 TTATATTTTAAATTTTAATATTTATAT-A-ATTTTAATATA-TTAATATACATAATAT
1033292 TTATATTTTAATATTT
1 TTATATTTTAA-ATTT
1033308 AAAAATATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
54 9 0.16
55 5 0.09
56 40 0.69
57 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (55 bp):
TTATATTTTAAATTTTAATATTTATATAATTTTAATATATTAATATACATAATAT
Found at i:1033323 original size:65 final size:65
Alignment explanation
Indices: 1033196--1033324 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 65
1033186 TTAAAATATT
* * * * *
1033196 TAATATTTTTATAATTTTAATATATTAATATTTATAATATATAAATTTTAAATTTTATATTTATA
1 TAATATTTTAATAATTTTAATATAATAATATTTATAATATATAAATTTAAAATATTAAATTTATA
* *
1033261 TAATATTTTAATAATTTT-ATATACATCATATTTAT-AT-TTTAATATTTAAAAATATTAAATTT
1 TAATATTTTAATAATTTTAATATA-ATAATATTTATAATATATAA-ATTT-AAAATATTAAATTT
1033323 AT
63 AT
1033325 TTAACATGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
63 4 0.07
64 11 0.20
65 39 0.72
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (65 bp):
TAATATTTTAATAATTTTAATATAATAATATTTATAATATATAAATTTAAAATATTAAATTTATA
Found at i:1036390 original size:22 final size:21
Alignment explanation
Indices: 1036359--1036399 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1036349 ATTTATAAAA
1036359 AAATTTAATAAATATAAATTT
1 AAATTTAATAAATATAAATTT
**
1036380 AAATCTTAATATTTATAAAT
1 AAAT-TTAATAAATATAAAT
1036400 CTAACCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTAATAAATATAAATTT
Found at i:1037419 original size:15 final size:16
Alignment explanation
Indices: 1037392--1037421 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1037382 TATCCATACT
1037392 TTGTGTAAGCAAAAAA
1 TTGTGTAAGCAAAAAA
1037408 TTGTGT-AGCAAAAA
1 TTGTGTAAGCAAAAA
1037422 TATTATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
TTGTGTAAGCAAAAAA
Found at i:1041339 original size:19 final size:18
Alignment explanation
Indices: 1041315--1041369 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1041305 TAAATTTAAT
* *
1041315 TATTTATGTATTTATATTA
1 TATTTATATATTT-TATAA
1041334 TATTTATATATTTTATAA
1 TATTTATATATTTTATAA
*
1041352 TATTTAAAATATTTTATA
1 TATTT-ATATATTTTATA
1041370 TTTATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 9 0.28
19 23 0.72
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTTATATATTTTATAA
Done.