Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 60 of 77
Found at i:12057775 original size:15 final size:15
Alignment explanation
Indices: 12057631--12057751 Score: 96
Period size: 15 Copynumber: 8.5 Consensus size: 15
12057621 AAATAATATT
*
12057631 ATAATATATTCATAA
1 ATAATATATTAATAA
12057646 ATAATATATTAATAA
1 ATAATATATTAATAA
* * *
12057661 ATATTATACTAATAT
1 ATAATATATTAATAA
*
12057676 ATTA-ATATTAATAA
1 ATAATATATTAATAA
*
12057690 ATAATAT-TGT-ATTA
1 ATAATATAT-TAATAA
12057704 ATAA-ATA--AATAA
1 ATAATATATTAATAA
12057716 CAT--TATATTAATAA
1 -ATAATATATTAATAA
* *
12057730 ATCATATATTAAGAA
1 ATAATATATTAATAA
12057745 ATAATAT
1 ATAATAT
12057752 TATAATATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 24 0.29
15 47 0.57
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATATATTAATAA
Found at i:12057781 original size:23 final size:23
Alignment explanation
Indices: 12057733--12057781 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12057723 TTAATAAATC
* *
12057733 ATATATTAAGAAATAATATTATA
1 ATATATTAAGAAATAATATAAAA
*
12057756 ATATATTAATAAATAATATAAAA
1 ATATATTAAGAAATAATATAAAA
12057779 ATA
1 ATA
12057782 ATAAATAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATATTAAGAAATAATATAAAA
Found at i:12057880 original size:9 final size:9
Alignment explanation
Indices: 12057863--12057935 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
12057853 ATTTATTTTT
*
12057863 TAATATTAA
1 TAATTTTAA
12057872 TAATTTTAA
1 TAATTTTAA
*
12057881 TAA--TAAA
1 TAATTTTAA
12057888 TAATTTTAA
1 TAATTTTAA
12057897 T-ATATTTAA
1 TAAT-TTTAA
*
12057906 TAA--TAAA
1 TAATTTTAA
12057913 TAATTTTTAA
1 TAA-TTTTAA
12057923 T-ATTTTAA
1 TAATTTTAA
12057931 TAATT
1 TAATT
12057936 ATATTAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
7 12 0.24
8 9 0.18
9 25 0.49
10 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATTTTAA
Found at i:12057880 original size:15 final size:15
Alignment explanation
Indices: 12057860--12057900 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
12057850 TCTATTTATT
*
12057860 TTTTAATATTAATAA
1 TTTTAATATAAATAA
12057875 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
12057891 TTTTAATATA
1 TTTTAATATA
12057901 TTTAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:12057896 original size:25 final size:24
Alignment explanation
Indices: 12057863--12057934 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 24
12057853 ATTTATTTTT
*
12057863 TAATATTAATAATTTTAATAATAAA
1 TAATTTTAAT-ATTTTAATAATAAA
12057888 TAATTTTAATATATTTAATAATAAA
1 TAATTTTAATAT-TTTAATAATAAA
12057913 TAATTTTTAATATTTTAATAAT
1 TAA-TTTTAATATTTTAATAAT
12057935 TATATTAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 2 0.05
25 33 0.75
26 9 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTTAATATTTTAATAATAAA
Found at i:12057918 original size:15 final size:15
Alignment explanation
Indices: 12057861--12057918 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
12057851 CTATTTATTT
*
12057861 TTTAAT-ATTAATAA
1 TTTAATAATAAATAA
12057875 TTTTAATAATAAATAA
1 -TTTAATAATAAATAA
12057891 TTT--TAAT--AT-A
1 TTTAATAATAAATAA
12057901 TTTAATAATAAATAA
1 TTTAATAATAAATAA
12057916 TTT
1 TTT
12057919 TTAATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
10 4 0.11
11 2 0.06
12 4 0.11
13 4 0.11
14 2 0.06
15 13 0.36
16 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATAATAAATAA
Found at i:12058025 original size:29 final size:31
Alignment explanation
Indices: 12057969--12058026 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12057959 GAAAAATAAA
*
12057969 TAAATAATAAAAATATTTTTATTAATTTATT
1 TAAATAATAAAAATATTATTATTAATTTATT
12058000 TAAATAATAAAAAT-TTATT-TTAATTTA
1 TAAATAATAAAAATATTATTATTAATTTA
12058027 AAAACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TAAATAATAAAAATATTATTATTAATTTATT
Found at i:12064971 original size:14 final size:14
Alignment explanation
Indices: 12064952--12064983 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12064942 ATTTACGTTT
12064952 ATTTTTTAAAATTA
1 ATTTTTTAAAATTA
*
12064966 ATTTTTTAAAATTT
1 ATTTTTTAAAATTA
12064980 ATTT
1 ATTT
12064984 ATTTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTTAAAATTA
Found at i:12065968 original size:21 final size:22
Alignment explanation
Indices: 12065938--12065989 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12065928 GATATTTTTA
12065938 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12065958 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12065980 AATATTTTAT
1 AATATTTTAT
12065990 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:12079880 original size:19 final size:19
Alignment explanation
Indices: 12079816--12079893 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 19
12079806 ATGTGATATG
*
12079816 ATATAATTAATATATTTAA
1 ATATAATTAATTTATTTAA
***
12079835 ATATAATTAAATTGTTGACTCGCA
1 ATATAATT-AA-T-TT-A-TTTAA
12079859 ATATAATTAATTTATTTAA
1 ATATAATTAATTTATTTAA
* *
12079878 ATATAAATAAGTTATT
1 ATATAATTAATTTATT
12079894 ATATATATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 24 0.53
20 3 0.07
21 3 0.07
22 2 0.04
23 3 0.07
24 10 0.22
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATAATTAATTTATTTAA
Found at i:12082195 original size:29 final size:29
Alignment explanation
Indices: 12082161--12082220 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
12082151 TTACTAACAT
12082161 AGTGAGAACAAAACTTTGTACTAGGATTA
1 AGTGAGAACAAAACTTTGTACTAGGATTA
*
12082190 AGTGAGAACGAAACTTTGTACTAGGATTA
1 AGTGAGAACAAAACTTTGTACTAGGATTA
12082219 AG
1 AG
12082221 ACTAAGGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (29 bp):
AGTGAGAACAAAACTTTGTACTAGGATTA
Found at i:12093095 original size:19 final size:20
Alignment explanation
Indices: 12093052--12093101 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
12093042 TGATATTTTT
12093052 AAATA-TTTATATTTAAAAA
1 AAATATTTTATATTTAAAAA
12093071 ATAATATTTTATA-TTAAAAA
1 A-AATATTTTATATTTAAAAA
12093091 AAATATTTTAT
1 AAATATTTTAT
12093102 TAATTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.38
20 12 0.41
21 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATTTTATATTTAAAAA
Found at i:12093941 original size:20 final size:20
Alignment explanation
Indices: 12093918--12093958 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12093908 ATTTTTTAAA
*
12093918 AATATGATTAAATTAAATTT
1 AATAAGATTAAATTAAATTT
* *
12093938 AATAAGATTATATTTAATTT
1 AATAAGATTAAATTAAATTT
12093958 A
1 A
12093959 CATGTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
AATAAGATTAAATTAAATTT
Found at i:12097014 original size:2 final size:2
Alignment explanation
Indices: 12096962--12096997 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12096952 CTACTACACA
12096962 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
12096998 CTCGTTGGTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12102196 original size:20 final size:21
Alignment explanation
Indices: 12102154--12102196 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12102144 ACTGTCTTTT
*
12102154 AAATAAAAAATCATAATTTTAA
1 AAATAAAAAA-CATAATTATAA
*
12102176 AAATAAAAAA-ATTATTATAA
1 AAATAAAAAACATAATTATAA
12102196 A
1 A
12102197 TATTGACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAAAAACATAATTATAA
Found at i:12102359 original size:67 final size:68
Alignment explanation
Indices: 12102250--12102389 Score: 237
Period size: 67 Copynumber: 2.1 Consensus size: 68
12102240 TTAGGAGGCA
* *
12102250 TTTGATTCTTTTTTCGAAATTTTATTATTAAGTATTTAATTTTAACATTTAATTTAAGATAATTT
1 TTTGATTCTTTTTTCGAAAATTTATTATTAAGTATTTAATTTTAACATTCAATTTAAGATAATTT
12102315 AAC
66 AAC
* *
12102318 TTTGATT-TTTTTTTGAAAATTTATTATTAAGTATTTGATTTTAACATTCAATTTAAGATAATTT
1 TTTGATTCTTTTTTCGAAAATTTATTATTAAGTATTTAATTTTAACATTCAATTTAAGATAATTT
12102382 AAC
66 AAC
12102385 TTTGA
1 TTTGA
12102390 AAAAAAAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
67 61 0.90
68 7 0.10
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (68 bp):
TTTGATTCTTTTTTCGAAAATTTATTATTAAGTATTTAATTTTAACATTCAATTTAAGATAATTT
AAC
Found at i:12102426 original size:67 final size:66
Alignment explanation
Indices: 12102265--12102426 Score: 166
Period size: 67 Copynumber: 2.4 Consensus size: 66
12102255 TTCTTTTTTC
* * *******
12102265 GAAATTTTATTATTAAGTATTTAATTTTAACATTTAATTTAAGATAATTTAACTTTGATTTTTTT
1 GAAAATTTATTA-TAAGTATTTAATTTTAACATTCAATTTAAGATAATTTAACTTTGAAAAAAAA
*
12102330 TT
65 GT
*
12102332 GAAAATTTATTATTAAGTATTTGATTTTAACATTCAATTTAAGATAATTTAACTTTGAAAAAAAA
1 GAAAATTTATTA-TAAGTATTTAATTTTAACATTCAATTTAAGATAATTTAACTTTGAAAAAAAA
12102397 GT
65 GT
12102399 GATAAATTT-TTA-ACAGTATTTAAATTTT
1 GA-AAATTTATTATA-AGTATTT-AATTTT
12102427 TGAAATTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.01
66 7 0.09
67 66 0.82
68 6 0.08
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (66 bp):
GAAAATTTATTATAAGTATTTAATTTTAACATTCAATTTAAGATAATTTAACTTTGAAAAAAAAG
T
Found at i:12102741 original size:62 final size:60
Alignment explanation
Indices: 12102624--12102741 Score: 150
Period size: 60 Copynumber: 1.9 Consensus size: 60
12102614 ATTTAACATG
* * * *
12102624 AAAAATATCTTAAATAATCATTTTAATTTTTTATAAGATTATTTGAGATATTTTTTGACA
1 AAAAATACCTTAAATAATCATTTTAATTTTTTATAAGATTATTTAAAACATTTTTTGACA
12102684 AAAAATACCTTAAATAATC-TTATTCAATTTTTT-TGAAAGATTATTTAAAACATTTTTT
1 AAAAATACCTTAAATAATCATT-TT-AATTTTTTAT--AAGATTATTTAAAACATTTTTT
12102742 ACCTCAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 2 0.04
60 21 0.42
61 8 0.16
62 19 0.38
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (60 bp):
AAAAATACCTTAAATAATCATTTTAATTTTTTATAAGATTATTTAAAACATTTTTTGACA
Found at i:12103277 original size:65 final size:66
Alignment explanation
Indices: 12103149--12103353 Score: 252
Period size: 62 Copynumber: 3.3 Consensus size: 66
12103139 AGTAAATGGT
* *
12103149 ATTATTTAAGACT-TTTTTTTTATAAAAAATACATTAAATAATCTAC--TT-AAAAAATATTAGA
1 ATTATTTAAGACTATTTTTTTTATAAAAAATACCTTAAATAATCTTCTTTTAAAAAAATATTAGA
12103210 G
66 G
* *
12103211 ATTATTTAAGA-TATTTTTTTTATCAAAAATGCCTTAAATAATCTTCTTTTAAAAAAATATTAGA
1 ATTATTTAAGACTATTTTTTTTATAAAAAATACCTTAAATAATCTTCTTTTAAAAAAATATTAGA
12103275 G
66 G
* * * * *
12103276 ATTATTTAA-AGTA--TTTTTGATAAAAAATATCTTAAGTAATC-TCTTTTAAAAAAA-ATTAAA
1 ATTATTTAAGACTATTTTTTTTATAAAAAATACCTTAAATAATCTTCTTTTAAAAAAATATTAGA
12103336 G
66 G
12103337 ATTATTTAAGAC-ATTTT
1 ATTATTTAAGACTATTTT
12103354 AAAACAAAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
61 17 0.14
62 54 0.44
63 25 0.20
64 3 0.02
65 25 0.20
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (66 bp):
ATTATTTAAGACTATTTTTTTTATAAAAAATACCTTAAATAATCTTCTTTTAAAAAAATATTAGA
G
Found at i:12103378 original size:62 final size:63
Alignment explanation
Indices: 12103244--12103378 Score: 159
Period size: 62 Copynumber: 2.2 Consensus size: 63
12103234 CAAAAATGCC
* * ** * * *
12103244 TTAAATAATCTTCTTTTAAAAAAATATTAGAGATTATTTAAAGTATTTTTGATAAAAAATATC
1 TTAAATAATCTTCTTTTAAAAAAATATTAAAGATTATTTAAAGCATTTTAAACAAAAAACATA
*
12103307 TTAAGTAATC-TCTTTTAAAAAAA-ATTAAAGATTATTT-AAGACATTTTAAAACAAAAAACATA
1 TTAAATAATCTTCTTTTAAAAAAATATTAAAGATTATTTAAAG-CATTTT-AAACAAAAAACATA
12103369 TTAAATAATC
1 TTAAATAATC
12103379 AATTAAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 3 0.05
61 18 0.30
62 31 0.51
63 9 0.15
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (63 bp):
TTAAATAATCTTCTTTTAAAAAAATATTAAAGATTATTTAAAGCATTTTAAACAAAAAACATA
Found at i:12103594 original size:18 final size:19
Alignment explanation
Indices: 12103571--12103618 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
12103561 AAAAAATTAT
12103571 AATTATATATATTA-AAAA
1 AATTATATATATTATAAAA
12103589 AATTATGATA-ATTATTAAAA
1 AATTAT-ATATATTA-TAAAA
12103609 AATTA-ATATA
1 AATTATATATA
12103619 AATAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 13 0.50
19 4 0.15
20 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTATATATATTATAAAA
Found at i:12103604 original size:21 final size:24
Alignment explanation
Indices: 12103561--12103610 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12103551 AAAAATGAAT
12103561 AAAAAATTATAATTATATATATTA
1 AAAAAATTATAATTATATATATTA
*
12103585 AAAAAATTATGA-TA-AT-TATTA
1 AAAAAATTATAATTATATATATTA
12103606 AAAAA
1 AAAAA
12103611 TTAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 2 0.08
24 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAAATTATAATTATATATATTA
Found at i:12104167 original size:32 final size:32
Alignment explanation
Indices: 12104046--12104185 Score: 89
Period size: 31 Copynumber: 4.5 Consensus size: 32
12104036 AATCCTCAAT
* *
12104046 AATATAA-ATATAATATATT-T-TAAATTATAA
1 AATATAATATATAA-ATTTTATATAAAATATAA
* * *
12104076 TAATAATTATATATAAA-ATTA-ATAAAATAAAA
1 -AAT-ATAATATATAAATTTTATATAAAATATAA
* * *
12104108 AATATAATTTAT-ATTTTTATAT-TAATATAA
1 AATATAATATATAAATTTTATATAAAATATAA
* *
12104138 ATTATAATATATAAATTTTATATAAAATATGA
1 AATATAATATATAAATTTTATATAAAATATAA
* *
12104170 TACA-AATATATAAATT
1 AATATAATATATAAATT
12104186 ATCATATCTA
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
29 1 0.01
30 26 0.31
31 32 0.38
32 19 0.23
33 6 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (32 bp):
AATATAATATATAAATTTTATATAAAATATAA
Found at i:12105021 original size:31 final size:32
Alignment explanation
Indices: 12104973--12105058 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 32
12104963 ATTTTCATTT
*
12104973 AAATATGA-ATTATAATATATAATT-TTTATATA
1 AAATATGATA-TA-AATATATAATTATTAATATA
*
12105005 AAATATGATATAAATATATAAATTATTAATATT
1 AAATATGATATAAATATAT-AATTATTAATATA
** *
12105038 TTATATTATATAAATATATAA
1 AAATATGATATAAATATATAA
12105059 ATGATCAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
31 7 0.15
32 16 0.35
33 23 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
AAATATGATATAAATATATAATTATTAATATA
Found at i:12108658 original size:17 final size:17
Alignment explanation
Indices: 12108636--12108669 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12108626 TGGATTAACA
12108636 TAATTTATGATAATCTG
1 TAATTTATGATAATCTG
*
12108653 TAATTTATTATAATCTG
1 TAATTTATGATAATCTG
12108670 ATCGATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (17 bp):
TAATTTATGATAATCTG
Found at i:12113757 original size:2 final size:2
Alignment explanation
Indices: 12113750--12113779 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12113740 ACATACATAG
12113750 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
12113780 TCTCTAAAAT
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:12120468 original size:22 final size:21
Alignment explanation
Indices: 12120421--12120468 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12120411 AATTTTTTGT
* *
12120421 ATAATTTTGGTAACCTTTTTA
1 ATAATTTTAGTAACCTTTCTA
*
12120442 ATAATTTTAGTACCCTTTGCTA
1 ATAATTTTAGTAACCTTT-CTA
12120464 ATAAT
1 ATAAT
12120469 AATAATAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
ATAATTTTAGTAACCTTTCTA
Found at i:12124483 original size:24 final size:25
Alignment explanation
Indices: 12124453--12124506 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
12124443 TGATAATAAC
12124453 AATTTCTGAA-TTTTTTCACTATAT
1 AATTTCTGAATTTTTTTCACTATAT
*
12124477 AATTTCTGAATTTTTTTCATTATAT
1 AATTTCTGAATTTTTTTCACTATAT
12124502 AATTT
1 AATTT
12124507 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (25 bp):
AATTTCTGAATTTTTTTCACTATAT
Found at i:12134413 original size:20 final size:20
Alignment explanation
Indices: 12134354--12134414 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
12134344 AATATTAAAA
* *
12134354 TTTTAATTTTAATAATCAAG
1 TTTTAATTTTAATGATCAAT
* ** * *
12134374 ATTT-ATTAGAATGTTGAAT
1 TTTTAATTTTAATGATCAAT
12134393 TTTTAATTTTAATGATCAAT
1 TTTTAATTTTAATGATCAAT
12134413 TT
1 TT
12134415 AAAAATTTGG
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTAATTTTAATGATCAAT
Found at i:12134725 original size:22 final size:22
Alignment explanation
Indices: 12134697--12134743 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
12134687 TATGGTGCAT
* *
12134697 AAATCAAAGTTTTAACACCAGG
1 AAATCAAAGATTTAACACCAAG
12134719 AAATCAAAGATTTAACACCAAG
1 AAATCAAAGATTTAACACCAAG
12134741 AAA
1 AAA
12134744 ATCATCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (22 bp):
AAATCAAAGATTTAACACCAAG
Found at i:12135409 original size:22 final size:23
Alignment explanation
Indices: 12135375--12135437 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
12135365 AAAATAAAAA
*
12135375 ATAA-TAATTAAATCAAT-TCTT-
1 ATAATTAACTAAATCAATAT-TTG
*
12135396 ATAATTAACTAAATTAATATTTG
1 ATAATTAACTAAATCAATATTTG
*
12135419 AT-ATTATCTAAATCAATAT
1 ATAATTAACTAAATCAATAT
12135438 CAAATCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.11
22 28 0.80
23 3 0.09
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAATTAACTAAATCAATATTTG
Found at i:12135506 original size:11 final size:11
Alignment explanation
Indices: 12135451--12135519 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
12135441 ATCAATTTTT
* *
12135451 AAATATTACTG
1 AAATATTATTA
12135462 AAATATTATTA
1 AAATATTATTA
* *
12135473 GAATAATATTA
1 AAATATTATTA
**
12135484 TCA-A-TA-TA
1 AAATATTATTA
12135492 AAATATTATTA
1 AAATATTATTA
*
12135503 AAATATTACTA
1 AAATATTATTA
12135514 AAATAT
1 AAATAT
12135520 CAAAAACAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 3 0.07
11 37 0.80
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (11 bp):
AAATATTATTA
Found at i:12136003 original size:15 final size:17
Alignment explanation
Indices: 12135973--12136004 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12135963 TTTAAAGTTA
12135973 ATAATTATTGTATTTAT
1 ATAATTATTGTATTTAT
12135990 ATAA-TATT-TATTTAT
1 ATAATTATTGTATTTAT
12136005 GTTAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATAATTATTGTATTTAT
Found at i:12154831 original size:21 final size:22
Alignment explanation
Indices: 12154805--12154847 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12154795 AAAGATAATA
12154805 TTTTTAAATATCAT-AATTATT
1 TTTTTAAATATCATCAATTATT
*
12154826 TTTTTAAATTTCATCAATTATT
1 TTTTTAAATATCATCAATTATT
12154848 ATATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAAATATCATCAATTATT
Found at i:12155370 original size:18 final size:18
Alignment explanation
Indices: 12155349--12155408 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
12155339 GGTCTATAAT
12155349 TTATAATATTAAATTTAA
1 TTATAATATTAAATTTAA
**
12155367 TTATTCT-TTATAATTTAA
1 TTATAATATTA-AATTTAA
**
12155385 TTATGCTTATATAAATTTAA
1 TTAT-AATAT-TAAATTTAA
12155405 TTAT
1 TTAT
12155409 GCATTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 16 0.47
19 1 0.03
20 12 0.35
21 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATAATATTAAATTTAA
Found at i:12155403 original size:20 final size:19
Alignment explanation
Indices: 12155358--12155418 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 19
12155348 TTTATAATAT
*
12155358 TAAATTTAATTATTCTTTA
1 TAAATTTAATTATGCTTTA
12155377 T-AATTTAATTATGCTTATA
1 TAAATTTAATTATGCTT-TA
12155396 TAAATTTAATTATGCATTTA
1 TAAATTTAATTATGC-TTTA
12155416 TAA
1 TAA
12155419 TATTAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
18 14 0.37
19 4 0.11
20 18 0.47
21 2 0.05
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (19 bp):
TAAATTTAATTATGCTTTA
Found at i:12155447 original size:25 final size:26
Alignment explanation
Indices: 12155396--12155449 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
12155386 TATGCTTATA
*
12155396 TAAATTTAATTATGCATTTATAATAT
1 TAAATTTAATAATGCATTTATAATAT
*
12155422 TAAATTT-ATAATGCTTTTATAATAT
1 TAAATTTAATAATGCATTTATAATAT
12155447 TAA
1 TAA
12155450 TAAATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAATTTAATAATGCATTTATAATAT
Found at i:12155454 original size:28 final size:27
Alignment explanation
Indices: 12155392--12155455 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
12155382 TAATTATGCT
*
12155392 TATATAAATTTAATTATGCATTTATAA
1 TATATAAATTTAATAATGCATTTATAA
*
12155419 TAT-TAAATTT-ATAATGCTTTTATAA
1 TATATAAATTTAATAATGCATTTATAA
12155444 TATTAATAAATT
1 TA-T-ATAAATT
12155456 ATGTCTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 15 0.47
26 8 0.25
27 3 0.09
28 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
TATATAAATTTAATAATGCATTTATAA
Found at i:12155463 original size:25 final size:25
Alignment explanation
Indices: 12155403--12155463 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
12155393 ATATAAATTT
* *
12155403 AATTATGCATTTATAATATTAAATT
1 AATTATGCTTTTATAATATTAAATA
* *
12155428 TATAATGCTTTTATAATATT-AATA
1 AATTATGCTTTTATAATATTAAATA
12155452 AATTATGTCTTT
1 AATTATG-CTTT
12155464 AACTTAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (25 bp):
AATTATGCTTTTATAATATTAAATA
Found at i:12155513 original size:24 final size:24
Alignment explanation
Indices: 12155485--12155531 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12155475 ATTTTGACGT
**
12155485 AATTTAATTATGCTTTTATAATTA
1 AATTTAATTATAATTTTATAATTA
12155509 AATTTAATTATAATTTTATAATT
1 AATTTAATTATAATTTTATAATT
12155532 TCATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AATTTAATTATAATTTTATAATTA
Found at i:12156597 original size:21 final size:20
Alignment explanation
Indices: 12156559--12156598 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12156549 ATTTTAAAAA
*
12156559 ACAAAATTAAATATATAAAG
1 ACAAAATTAAATAAATAAAG
*
12156579 ACAAAATTTAATAAAATAAA
1 ACAAAATTAAAT-AAATAAA
12156599 AAACAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (20 bp):
ACAAAATTAAATAAATAAAG
Found at i:12166464 original size:3 final size:3
Alignment explanation
Indices: 12166456--12166500 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12166446 TTTTATGATG
12166456 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12166501 AAAAACAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12166715 original size:8 final size:8
Alignment explanation
Indices: 12166680--12166729 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
12166670 AATTTTTGCT
12166680 AAAAAATA
1 AAAAAATA
*
12166688 AAAAATTA
1 AAAAAATA
12166696 TAAAAAATA
1 -AAAAAATA
*
12166705 AAATAAAAA
1 AAA-AAATA
12166714 AATAAAATA
1 AA-AAAATA
12166723 AAAAAAT
1 AAAAAAT
12166730 TGTTTAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 15 0.43
9 19 0.54
10 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:12166715 original size:13 final size:13
Alignment explanation
Indices: 12166697--12166729 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12166687 AAAAAATTAT
12166697 AAAAAATAAAATA
1 AAAAAATAAAATA
12166710 AAAAAATAAAATA
1 AAAAAATAAAATA
12166723 AAAAAAT
1 AAAAAAT
12166730 TGTTTAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:12167435 original size:3 final size:3
Alignment explanation
Indices: 12167427--12167451 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12167417 TAGAATACAA
12167427 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
12167452 TTGTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12169542 original size:130 final size:130
Alignment explanation
Indices: 12169309--12169568 Score: 421
Period size: 130 Copynumber: 2.0 Consensus size: 130
12169299 GGCTTAAGCT
* *
12169309 CTAACCAAAATTATCTCAAAATCTTAAAGACACATACGAAAATCTTAAGTGGAGTAATTTGTTCT
1 CTAACCAAAACTATCTCAAAATCCTAAAGACACATACGAAAATCTTAAGTGGAGTAATTTGTTCT
* * *
12169374 CGAATGCTGCCTAGATAATGGGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTCTCATGAGTC
66 CGAATGCTACCTAGATAATGAGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTCTCACGAGTC
* ** **
12169439 CTAACCAAAACTATCTCAAAATCCTAAGGACATGTGTGAAAATCTTAAGTGGAGTAATTTGTTCT
1 CTAACCAAAACTATCTCAAAATCCTAAAGACACATACGAAAATCTTAAGTGGAGTAATTTGTTCT
*
12169504 CGAATGCTACCTAGATGATGAGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTCTCACGAGTC
66 CGAATGCTACCTAGATAATGAGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTCTCACGAGTC
12169569 TTTAATTCGC
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (130 bp):
CTAACCAAAACTATCTCAAAATCCTAAAGACACATACGAAAATCTTAAGTGGAGTAATTTGTTCT
CGAATGCTACCTAGATAATGAGGTATTTAAAGAAATCTTATTCCATTAAGTTTTTCTCACGAGTC
Found at i:12169626 original size:17 final size:17
Alignment explanation
Indices: 12169604--12169636 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12169594 AATAATTGTT
12169604 TAATAAAAAAATAAGAA
1 TAATAAAAAAATAAGAA
*
12169621 TAATAATAAAATAAGA
1 TAATAAAAAAATAAGA
12169637 TTTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
TAATAAAAAAATAAGAA
Found at i:12170560 original size:41 final size:41
Alignment explanation
Indices: 12170447--12170756 Score: 264
Period size: 41 Copynumber: 7.3 Consensus size: 41
12170437 CCATTACGAC
* * * *
12170447 ATTTAGAGGAGCCTTTTATCTTTTAAAAGTTATTGTGCCTCT
1 ATTTAAAGGAG-CATTTATTTTTTAAAAGTTGTTGTGCCTCT
* * * *
12170489 ATTTAAAAGAGCCTTTTATTTTTTAAAAGTTGTGGTGCCTTT
1 ATTTAAAGGAG-CATTTATTTTTTAAAAGTTGTTGTGCCTCT
* *
12170531 ATTTAGAGGAGCATTTATTTTTTAAAAGTTGTGGTGCCTCT
1 ATTTAAAGGAGCATTTATTTTTTAAAAGTTGTTGTGCCTCT
* * * *
12170572 GTTTAAATGAGCATTTATTTTTCAAAAGTTGTTGTG-CTGTT
1 ATTTAAAGGAGCATTTATTTTTTAAAAGTTGTTGTGCCT-CT
* **
12170613 TTTTAAAAAAGCATTTATTTTTTCAAAAGTTAAAAAGTTGTGGTGCCTCT
1 ATTTAAAGGAGCATTTATTTTTT-AAAAGTT-----G-T-T-GTGCCTCT
*
12170663 ATTTAAAGGAGTATTTATTTTTTAAAAGTTGTTGTGCCTCT
1 ATTTAAAGGAGCATTTATTTTTTAAAAGTTGTTGTGCCTCT
* * * * *
12170704 ATTTAGAGGAGC-TTTTTATTTTTCAAAGTTGTTGAGCCTTT
1 ATTTAAAGGAGCATTTAT-TTTTTAAAAGTTGTTGTGCCTCT
* *
12170745 GTTTAGAGGAGC
1 ATTTAAAGGAGC
12170757 TTGATTTATT
Statistics
Matches: 224, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
40 6 0.03
41 128 0.57
42 53 0.24
43 1 0.00
44 1 0.00
47 1 0.00
48 1 0.00
49 8 0.04
50 23 0.10
51 2 0.01
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (41 bp):
ATTTAAAGGAGCATTTATTTTTTAAAAGTTGTTGTGCCTCT
Found at i:12170757 original size:41 final size:42
Alignment explanation
Indices: 12170645--12170777 Score: 146
Period size: 41 Copynumber: 3.2 Consensus size: 42
12170635 TCAAAAGTTA
* * *
12170645 AAAAGTTGTGGTGCCTCTATTTAAAGGAG--TATTTATTTTTT
1 AAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTATTTA-TTTTT
*
12170686 AAAAGTTGTTGTGCCTCTATTTAGAGGAGCTT-TTTATTTTT
1 AAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTATTTATTTTT
* * * *
12170727 CAAAGTTGTTGAGCCTTTGTTTAGAGGAGCTTGATTTATTTTA
1 AAAAGTTGTTGAGCCTCTATTTAGAGGAGCTT-ATTTATTTTT
12170770 AATAAGTT
1 AA-AAGTT
12170778 TTTATGTTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
41 60 0.76
42 4 0.05
43 10 0.13
44 5 0.06
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (42 bp):
AAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTATTTATTTTT
Found at i:12171267 original size:5 final size:5
Alignment explanation
Indices: 12171257--12171283 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12171247 ATCTTTGTCT
12171257 CAAGC CAAGC CAAGC CAAGC CAAGC CA
1 CAAGC CAAGC CAAGC CAAGC CAAGC CA
12171284 CTTTTTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.41, G:0.19, T:0.00
Consensus pattern (5 bp):
CAAGC
Found at i:12175563 original size:21 final size:21
Alignment explanation
Indices: 12175537--12175611 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
12175527 TTATTAATCA
12175537 TATTTTTAAATTAATAAAAAT
1 TATTTTTAAATTAATAAAAAT
* *
12175558 TATTTTT--ATTAACAAAGATT
1 TATTTTTAAATTAATAAA-AAT
* *
12175578 ATATTTTTAAATATCATAAATA-
1 -TATTTTTAAAT-TAATAAAAAT
12175600 TATTTTTAAATT
1 TATTTTTAAATT
12175612 TCATCAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
19 8 0.19
20 3 0.07
21 25 0.58
23 2 0.05
24 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (21 bp):
TATTTTTAAATTAATAAAAAT
Found at i:12175578 original size:19 final size:20
Alignment explanation
Indices: 12175546--12175584 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
12175536 ATATTTTTAA
*
12175546 ATTAATAAAAATTAT-TTTT
1 ATTAACAAAAATTATATTTT
*
12175565 ATTAACAAAGATTATATTTT
1 ATTAACAAAAATTATATTTT
12175585 TAAATATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTAACAAAAATTATATTTT
Found at i:12175615 original size:21 final size:21
Alignment explanation
Indices: 12175577--12175623 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
12175567 TAACAAAGAT
12175577 TATATTTTTAAATATCATAAA
1 TATATTTTTAAATATCATAAA
* *
12175598 TATATTTTTAAATTTCATCAA
1 TATATTTTTAAATATCATAAA
12175619 T-TATT
1 TATATT
12175624 ACATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTTTTAAATATCATAAA
Found at i:12176134 original size:44 final size:43
Alignment explanation
Indices: 12176086--12176234 Score: 152
Period size: 44 Copynumber: 3.6 Consensus size: 43
12176076 AGTACCTGAT
12176086 AATTTAATTATG-TTTTTAATTTAAGTCTATAATTTATAATATTA
1 AATTTAATTATGCTTTTTAATTTAA-T-TATAATTTATAATATTA
* * **
12176130 AATTTATTTATGCTTTATAATTTAATTATGTTTTTATAATATTA
1 AATTTAATTATGCTTTTTAATTTAATTAT-AATTTATAATATTA
*
12176174 AATTT-ATAATGCTTTTATAA--T-ATTA-AATTTATAATATT-
1 AATTTAATTATGCTTTT-TAATTTAATTATAATTTATAATATTA
*
12176212 AATTAAATTATG-TTTTTAATTTA
1 AATTTAATTATGCTTTTTAATTTA
12176235 GGTCTATTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
37 3 0.03
38 8 0.09
39 17 0.20
41 4 0.05
42 1 0.01
43 11 0.13
44 32 0.37
45 11 0.13
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (43 bp):
AATTTAATTATGCTTTTTAATTTAATTATAATTTATAATATTA
Found at i:12176148 original size:25 final size:25
Alignment explanation
Indices: 12176118--12176205 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
12176108 AAGTCTATAA
12176118 TTTATAATATTAAATTTATTTATGC
1 TTTATAATATTAAATTTATTTATGC
*
12176143 TTTATAAT-TT-AA-TTATGT-T--
1 TTTATAATATTAAATTTATTTATGC
*
12176162 TTTATAATATTAAATTTA-TAATGC
1 TTTATAATATTAAATTTATTTATGC
12176186 TTTTATAATATTAAATTTAT
1 -TTTATAATATTAAATTTAT
12176206 AATATTAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
19 8 0.15
20 2 0.04
21 3 0.06
22 9 0.17
23 2 0.04
24 2 0.04
25 26 0.50
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (25 bp):
TTTATAATATTAAATTTATTTATGC
Found at i:12176151 original size:18 final size:19
Alignment explanation
Indices: 12176130--12176174 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12176120 TATAATATTA
*
12176130 AATTTATTTATG-CTTTAT
1 AATTTAATTATGTCTTTAT
*
12176148 AATTTAATTATGTTTTTAT
1 AATTTAATTATGTCTTTAT
12176167 AATATTAA
1 AAT-TTAA
12176175 ATTTATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 8 0.35
20 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTAATTATGTCTTTAT
Found at i:12176179 original size:14 final size:14
Alignment explanation
Indices: 12176162--12176213 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
12176152 TAATTATGTT
12176162 TTTATAATATTAAA
1 TTTATAATATTAAA
**
12176176 TTTATAATGCT---
1 TTTATAATATTAAA
12176187 TTTATAATATTAAA
1 TTTATAATATTAAA
12176201 TTTATAATATTAA
1 TTTATAATATTAA
12176214 TTAAATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 9 0.29
14 22 0.71
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
TTTATAATATTAAA
Found at i:12176779 original size:22 final size:25
Alignment explanation
Indices: 12176734--12176781 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
12176724 TGATTAAATT
*
12176734 TATTATATTTTCAATTAAATTTAAA
1 TATTATATTTTCAATTAAAATTAAA
12176759 TATTA-ATTTT-AA-TAAAATTAAA
1 TATTATATTTTCAATTAAAATTAAA
12176781 T
1 T
12176782 CAATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 5 0.23
25 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTATATTTTCAATTAAAATTAAA
Found at i:12179517 original size:12 final size:12
Alignment explanation
Indices: 12179487--12179517 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12179477 ACCACCATCC
*
12179487 CCACCAAGAGCA
1 CCACCACGAGCA
12179499 CCACCACGAGCA
1 CCACCACGAGCA
12179511 CCACCAC
1 CCACCAC
12179518 CGCCTTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.52, G:0.13, T:0.00
Consensus pattern (12 bp):
CCACCACGAGCA
Found at i:12182146 original size:52 final size:52
Alignment explanation
Indices: 12182060--12182163 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
12182050 GGATAAGAAG
*
12182060 ACTTGCAAAAGAAGAATTCTAAGAAAAAAGAGATTCTTAATAGACAAGTTTA
1 ACTTGCAAAAGAAAAATTCTAAGAAAAAAGAGATTCTTAATAGACAAGTTTA
* *
12182112 ACTTGCAAAAGAAAAATTTTAAGAGGAAAA-AGATTCTTAATAGACAAGTTTA
1 ACTTGCAAAAGAAAAATTCTAAGA-AAAAAGAGATTCTTAATAGACAAGTTTA
12182164 TATGGTTACA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 44 0.92
53 4 0.08
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (52 bp):
ACTTGCAAAAGAAAAATTCTAAGAAAAAAGAGATTCTTAATAGACAAGTTTA
Found at i:12193437 original size:21 final size:21
Alignment explanation
Indices: 12193413--12193480 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
12193403 TAACAAAGAT
12193413 TATATTTTTAAATATCATAAA
1 TATATTTTTAAATATCATAAA
12193434 TATATTTTTAAATATCATAAA
1 TATATTTTTAAATATCATAAA
* *
12193455 TATATTTTTAAATTTCATCAA
1 TATATTTTTAAATATCATAAA
12193476 T-TATT
1 TATATT
12193481 ATATTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.09
21 41 0.91
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTTTTAAATATCATAAA
Found at i:12194083 original size:6 final size:6
Alignment explanation
Indices: 12194072--12194098 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12194062 CCATCCCCAC
12194072 CACGAG CACGAG CACGAG CACGAG CAC
1 CACGAG CACGAG CACGAG CACGAG CAC
12194099 CACCACCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.30, T:0.00
Consensus pattern (6 bp):
CACGAG
Found at i:12194277 original size:3 final size:3
Alignment explanation
Indices: 12194271--12194322 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
12194261 TTCTGTGGAA
12194271 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12194319 ATT A
1 ATT A
12194323 AAACAATTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12194539 original size:3 final size:3
Alignment explanation
Indices: 12194531--12194573 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12194521 CTTTTACAAA
12194531 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12194574 GACCGAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12195413 original size:21 final size:21
Alignment explanation
Indices: 12195384--12195425 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12195374 AAAAGTATCA
*
12195384 CAACCAATTCCATATTCAATC
1 CAACCAATTCCACATTCAATC
*
12195405 CAACTAATTCCACATTCAATC
1 CAACCAATTCCACATTCAATC
12195426 ACCATAACAG
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:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (21 bp):
CAACCAATTCCACATTCAATC
Found at i:12200846 original size:24 final size:26
Alignment explanation
Indices: 12200819--12200869 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
12200809 TTTATATTTT
12200819 TTTTTA-CTAACTGTTACAGTGA-TG
1 TTTTTATCTAACTGTTACAGTGACTG
* *
12200843 -TTTTATTTATCTGTTACAGTGACTG
1 TTTTTATCTAACTGTTACAGTGACTG
12200868 TT
1 TT
12200870 ACAATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.23
24 14 0.64
25 2 0.09
26 1 0.05
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.51
Consensus pattern (26 bp):
TTTTTATCTAACTGTTACAGTGACTG
Found at i:12205170 original size:7 final size:7
Alignment explanation
Indices: 12205158--12205220 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
12205148 CACGTATATA
12205158 TAAAAAT
1 TAAAAAT
12205165 TAAAAA-
1 TAAAAAT
12205171 T-AAAAT
1 TAAAAAT
* *
12205177 TATATAT
1 TAAAAAT
12205184 GTAAAAAT
1 -TAAAAAT
12205192 TAAAAAT
1 TAAAAAT
12205199 TAAAAAT
1 TAAAAAT
*
12205206 ATATAAAAA
1 -TA-AAAAT
12205215 TAAAAA
1 TAAAAA
12205221 ATAAGTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
5 4 0.09
6 2 0.04
7 27 0.59
8 9 0.20
9 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
TAAAAAT
Found at i:12205188 original size:27 final size:24
Alignment explanation
Indices: 12205152--12205224 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 24
12205142 TTAATTCACG
12205152 TATATATAAAAATTAAAAATAAAATTA
1 TATAT-TAAAAATTAAAAATAAAA--A
12205179 TATATGTAAAAATTAAAAATTAAAAA
1 TATAT-TAAAAATTAAAAA-TAAAAA
*
12205205 TATA-TAAAAATAAAAAATAA
1 TATATTAAAAATTAAAAATAA
12205225 GTTTAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.07
24 12 0.28
26 5 0.12
27 18 0.42
28 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (24 bp):
TATATTAAAAATTAAAAATAAAAA
Found at i:12206317 original size:18 final size:18
Alignment explanation
Indices: 12206251--12206315 Score: 105
Period size: 18 Copynumber: 3.6 Consensus size: 18
12206241 CCATCTAATA
12206251 TAGAAAATATTTAATTTTT
1 TAGAAAAT-TTTAATTTTT
12206270 TAGAAAATTTTAATTTTT
1 TAGAAAATTTTAATTTTT
12206288 TAGAAAATTTTAATTTTT
1 TAGAAAATTTTAATTTTT
*
12206306 CA-AAAATTTT
1 TAGAAAATTTT
12206316 TAGTGCCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 8 0.18
18 29 0.64
19 8 0.18
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
TAGAAAATTTTAATTTTT
Found at i:12206395 original size:17 final size:17
Alignment explanation
Indices: 12206375--12206408 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12206365 ATATATAATT
*
12206375 AATTATTAATAATATTA
1 AATTAATAATAATATTA
*
12206392 AATTAATAATATTATTA
1 AATTAATAATAATATTA
12206409 TTATCATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAATAATAATATTA
Found at i:12206396 original size:14 final size:14
Alignment explanation
Indices: 12206379--12206405 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12206369 ATAATTAATT
12206379 ATTAATAATATTAA
1 ATTAATAATATTAA
12206393 ATTAATAATATTA
1 ATTAATAATATTA
12206406 TTATTATCAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATAATATTAA
Found at i:12207422 original size:31 final size:29
Alignment explanation
Indices: 12207381--12207471 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 29
12207371 AGAGGTACTA
12207381 AAATTTAAATTTTATGCGAGTATAAGAACT
1 AAATTTAAATTTTAT-CGAGTATAAGAACT
* * * *
12207411 AAATTTCAAATTTCATTCCAATATAA-AGATT
1 AAATTT-AAATTTTA-TCGAGTATAAGA-ACT
*
12207442 AAATTTTAAATTGTAT-GAGTATAAGAACT
1 AAA-TTTAAATTTTATCGAGTATAAGAACT
12207471 A
1 A
12207472 TTTGTATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
29 9 0.19
30 9 0.19
31 25 0.53
32 4 0.09
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (29 bp):
AAATTTAAATTTTATCGAGTATAAGAACT
Found at i:12207533 original size:19 final size:19
Alignment explanation
Indices: 12207509--12207548 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12207499 TAATTTTAAT
*
12207509 TATCACATCAATAAATCAA
1 TATCACATCAAAAAATCAA
*
12207528 TATCACATTAAAAAATCAA
1 TATCACATCAAAAAATCAA
12207547 TA
1 TA
12207549 ACCACATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (19 bp):
TATCACATCAAAAAATCAA
Found at i:12207634 original size:17 final size:17
Alignment explanation
Indices: 12207612--12207645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12207602 AAATTATCAA
12207612 ATTAAAATAATATAAAT
1 ATTAAAATAATATAAAT
* *
12207629 ATTAAATTTATATAAAT
1 ATTAAAATAATATAAAT
12207646 TATATTATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAATAATATAAAT
Found at i:12208675 original size:20 final size:21
Alignment explanation
Indices: 12208650--12208692 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12208640 AAAAAAGATG
12208650 AAATAAAAA-A-TTAAATATAA
1 AAATAAAAACATTTAAAT-TAA
12208670 AAATAAAAACATTTAAATTAA
1 AAATAAAAACATTTAAATTAA
12208691 AA
1 AA
12208693 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAAAAACATTTAAATTAA
Found at i:12223660 original size:10 final size:10
Alignment explanation
Indices: 12223647--12223673 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12223637 TTTTGTTCAG
12223647 TTTTTTTTAT
1 TTTTTTTTAT
12223657 TTTTTTTTAT
1 TTTTTTTTAT
12223667 TTTTTTT
1 TTTTTTT
12223674 ATCTTAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:12224141 original size:25 final size:25
Alignment explanation
Indices: 12224099--12224151 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
12224089 AAGGATAACA
*
12224099 AATTTTTTAAAGAGTAAAAAAATTT
1 AATTTTTTAAAGAATAAAAAAATTT
*
12224124 AATTATTTTAAA-AATAAAAAATTTT
1 AATT-TTTTAAAGAATAAAAAAATTT
12224149 AAT
1 AAT
12224152 CAAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
AATTTTTTAAAGAATAAAAAAATTT
Found at i:12224170 original size:18 final size:19
Alignment explanation
Indices: 12224133--12224173 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
12224123 TAATTATTTT
12224133 AAAAATAAAAAATTTTAATC
1 AAAAATAAAAAA-TTTAATC
*
12224153 AAAAATTAAAAA-TTAATC
1 AAAAATAAAAAATTTAATC
12224171 AAA
1 AAA
12224174 TAGTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAAAAAATTTAATC
Found at i:12224275 original size:16 final size:17
Alignment explanation
Indices: 12224254--12224295 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
12224244 GATGTTAGGA
*
12224254 AATTAAAGATT-AAATT
1 AATTAAAAATTAAAATT
12224270 AATTAAAAATTAAAAATT
1 AATTAAAAATT-AAAATT
12224288 AATTAAAA
1 AATTAAAA
12224296 GAAAGGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
18 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTAAAAATTAAAATT
Found at i:12224882 original size:3 final size:3
Alignment explanation
Indices: 12224874--12224905 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12224864 TTCTTAAACA
12224874 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12224906 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12227959 original size:14 final size:15
Alignment explanation
Indices: 12227942--12227984 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
12227932 TTTATTATAT
12227942 ATAAT-TAATTATTA
1 ATAATATAATTATTA
*
12227956 ATAATATCA-TATTA
1 ATAATATAATTATTA
*
12227970 ATAATATTATTATTA
1 ATAATATAATTATTA
12227985 TCATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAATATAATTATTA
Found at i:12228812 original size:44 final size:44
Alignment explanation
Indices: 12228780--12228913 Score: 250
Period size: 44 Copynumber: 3.0 Consensus size: 44
12228770 GTGACAAAAT
12228780 ATTATGATAGATTTTTCGATATTGTAATAAAATATTATTAGAGA
1 ATTATGATAGATTTTTCGATATTGTAATAAAATATTATTAGAGA
*
12228824 ATTATGATAGATTTTTTGATATTGTAATAAAATATTATTAGAGA
1 ATTATGATAGATTTTTCGATATTGTAATAAAATATTATTAGAGA
*
12228868 ATTATGATAGATTTTTCAATATTGTAATAAAATATTATTAGAGA
1 ATTATGATAGATTTTTCGATATTGTAATAAAATATTATTAGAGA
12228912 AT
1 AT
12228914 AATATTATTG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 87 1.00
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (44 bp):
ATTATGATAGATTTTTCGATATTGTAATAAAATATTATTAGAGA
Found at i:12229337 original size:24 final size:24
Alignment explanation
Indices: 12229308--12229357 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12229298 CATAATTTGA
* *
12229308 CTTAATTTATTACTGTTCTTTTCT
1 CTTAATTAATTACTATTCTTTTCT
12229332 CTTAATTAATTACTATTCTTTTCT
1 CTTAATTAATTACTATTCTTTTCT
12229356 CT
1 CT
12229358 CACTTAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.60
Consensus pattern (24 bp):
CTTAATTAATTACTATTCTTTTCT
Found at i:12231325 original size:22 final size:22
Alignment explanation
Indices: 12231299--12231344 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12231289 AATATGGGAG
*
12231299 AACGAAATTATGTAATAAATTA
1 AACGAAATTATGTAACAAATTA
12231321 AACGAAATTATGTAACAAATTA
1 AACGAAATTATGTAACAAATTA
12231343 AA
1 AA
12231345 ATTTCTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.28
Consensus pattern (22 bp):
AACGAAATTATGTAACAAATTA
Found at i:12235631 original size:11 final size:10
Alignment explanation
Indices: 12235609--12235638 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
12235599 GTGTATAAAA
12235609 TTTTAATAAT
1 TTTTAATAAT
12235619 TTTTAATATAT
1 TTTTAATA-AT
12235630 TTTTAATAA
1 TTTTAATAA
12235639 AAATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:12237172 original size:60 final size:60
Alignment explanation
Indices: 12237105--12237224 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
12237095 AAAGAAACAA
* *
12237105 AGTCGCCAAGTTGGAAATTTCTTGCTCTAGGTCGCTCAGAATCCACTACACGACCTTGAC
1 AGTCGCCAAGTTGGAAATATCTTGCTCTAGGTCGCTCAGAATCCACTACACAACCTTGAC
* **
12237165 AGTCGCCAAGTTGGAAATATCTTGCTCTAGGTTGCTTGGAATCCACTACACAACCTTGAC
1 AGTCGCCAAGTTGGAAATATCTTGCTCTAGGTCGCTCAGAATCCACTACACAACCTTGAC
12237225 TTTGACTAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (60 bp):
AGTCGCCAAGTTGGAAATATCTTGCTCTAGGTCGCTCAGAATCCACTACACAACCTTGAC
Found at i:12240164 original size:27 final size:26
Alignment explanation
Indices: 12240149--12240199 Score: 59
Period size: 27 Copynumber: 1.9 Consensus size: 26
12240139 TTTATGAATA
*
12240149 TAATATATAA-ATATAAATTTTAATAAA
1 TAATAAATAATATAT-AATTTT-ATAAA
*
12240176 TAATAAATAATATATACTTTTATA
1 TAATAAATAATATATAATTTTATA
12240200 TGTATCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
26 3 0.14
27 14 0.67
28 4 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATAAATAATATATAATTTTATAAA
Found at i:12240352 original size:25 final size:24
Alignment explanation
Indices: 12240299--12240352 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12240289 AATTTAAAAA
* *
12240299 TATTTAATATTATTAAATTTGAAT
1 TATTTAATATTATTAAATATAAAT
* *
12240323 AATTTAAATTTTATTAAATATAAAT
1 TATTT-AATATTATTAAATATAAAT
12240348 TATTT
1 TATTT
12240353 TATCACTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTTAATATTATTAAATATAAAT
Found at i:12241609 original size:17 final size:17
Alignment explanation
Indices: 12241587--12241628 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
12241577 GAAAATTTTA
*
12241587 TTAAATTATTTTAATAT
1 TTAAATTATTTTAAAAT
12241604 TTAAATTATTTTAAAAT
1 TTAAATTATTTTAAAAT
*
12241621 TAAAATTA
1 TTAAATTA
12241629 AATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTATTTTAAAAT
Found at i:12245628 original size:80 final size:80
Alignment explanation
Indices: 12245514--12245675 Score: 261
Period size: 80 Copynumber: 2.0 Consensus size: 80
12245504 CTGGGTGTTA
*
12245514 CAGGGTTTACAGGATTAACGAGGTGAATAGGGGGTGGTAGTGGTAAACAAGGGTGAACAAGGGGT
1 CAGGGTTTACAGGATTAACGAGGTGAATAAGGGGTGGTAGTGGTAAACAAGGGTGAACAAGGGGT
*
12245579 GGTAGTGGTGCCAAG
66 CGTAGTGGTGCCAAG
** * * *
12245594 CAGGGTTTGTAGGATTAACGAGGTGAATAAGGGGTGGTAGTGGTAAATAGGGGTGAACAGGGGGT
1 CAGGGTTTACAGGATTAACGAGGTGAATAAGGGGTGGTAGTGGTAAACAAGGGTGAACAAGGGGT
12245659 CGTAGTGGTGCCAAG
66 CGTAGTGGTGCCAAG
12245674 CA
1 CA
12245676 TGACACCCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.28, C:0.09, G:0.43, T:0.21
Consensus pattern (80 bp):
CAGGGTTTACAGGATTAACGAGGTGAATAAGGGGTGGTAGTGGTAAACAAGGGTGAACAAGGGGT
CGTAGTGGTGCCAAG
Found at i:12245744 original size:24 final size:24
Alignment explanation
Indices: 12245707--12245761 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12245697 AGCTTTTTTG
* *
12245707 TTTT-TTTTTGTATTTTTCTCT-TT
1 TTTTGTTTTTATATTTTT-TATATT
12245730 TTTTGTTTTTATATTTTTTATATT
1 TTTTGTTTTTATATTTTTTATATT
12245754 TTTTGTTT
1 TTTTGTTT
12245762 AATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.09, C:0.04, G:0.05, T:0.82
Consensus pattern (24 bp):
TTTTGTTTTTATATTTTTTATATT
Found at i:12253798 original size:21 final size:19
Alignment explanation
Indices: 12253768--12253806 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
12253758 TTTATTTGAA
12253768 AAAGTTAATAATAATAAAAG
1 AAAGTTAATAATAA-AAAAG
12253788 AAAGTTTAATAATAAAAAA
1 AAAG-TTAATAATAAAAAA
12253807 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAGTTAATAATAAAAAAG
Found at i:12258508 original size:2 final size:2
Alignment explanation
Indices: 12258501--12258525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12258491 CAATCAAGTG
12258501 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 A
12258526 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12258530 original size:2 final size:2
Alignment explanation
Indices: 12258525--12258563 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12258515 ATATATATAT
12258525 AG AG AG AG 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 AG AG AG AG A
12258564 AAAGATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12259217 original size:252 final size:254
Alignment explanation
Indices: 12258766--12259265 Score: 898
Period size: 252 Copynumber: 2.0 Consensus size: 254
12258756 TTAACTCATA
12258766 TATATATATTCTCTTTCTGACAGAGCCTTAAAGGAAGTTGATTTATTTCCAACTTGTCTTTAGGA
1 TATATATATTCTCTTTCTGACAGAGCCTTAAAGGAAGTTGATTTATTTCCAACTTGTCTTTAGGA
* *
12258831 GTCTAACTTTATGGATGGCCACTAGGCATACGACTTTTTTTTCGGTTGTTTTTAAGTATAGGAAT
66 GTCTAACTTTATAGATGGCCACCAGGCATACGACTTTTTTTTCGGTTG---TT-A-TATAGGAAT
12258896 GGAGAGCTAGACCAAAGCATATAGCAGACTTTGGATCCACCACACGACCTTAACTTTGGCTATCC
126 GGAGAGCTAGACCAAAGCATATAGCAGACTTTGGATCCACCACACGACCTTAACTTTGGCTATCC
12258961 AAGACAATGAATAATTAATTATAAGCGTTGAGTTGCCAATATATTAGCTAGTTATATTAACTCG
191 AAGACAATGAATAATTAATTATAAGCGTTGAGTTGCCAATATATTAGCTAGTTATATTAACTCG
12259025 TATATATATTCTCTTTCTGACAGAGCCTTAAAGGAAGTTGATTTATTTCCAACTTGTCTTTAGGA
1 TATATATATTCTCTTTCTGACAGAGCCTTAAAGGAAGTTGATTTATTTCCAACTTGTCTTTAGGA
12259090 GTCTTAACTTTATAGATGGCCACCAGGCATACGACTTTTTTTTCGGTTG-T-T-TAGGAATGGAG
66 GTC-TAACTTTATAGATGGCCACCAGGCATACGACTTTTTTTTCGGTTGTTATATAGGAATGGAG
*
12259152 AGCTAGACCAAAGCATATCGCAGACTTTGGATCCACCACACGACCTTAACTTTGGCTATCCAAGA
130 AGCTAGACCAAAGCATATAGCAGACTTTGGATCCACCACACGACCTTAACTTTGGCTATCCAAGA
12259217 CAATGAATAATTAATTATAAGCGTTGAGTTGCCAATATATTAGCTAGTT
195 CAATGAATAATTAATTATAAGCGTTGAGTTGCCAATATATTAGCTAGTT
12259266 CAAAGACAAT
Statistics
Matches: 237, Mismatches: 3, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
252 124 0.52
253 1 0.00
256 1 0.00
259 68 0.29
260 43 0.18
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (254 bp):
TATATATATTCTCTTTCTGACAGAGCCTTAAAGGAAGTTGATTTATTTCCAACTTGTCTTTAGGA
GTCTAACTTTATAGATGGCCACCAGGCATACGACTTTTTTTTCGGTTGTTATATAGGAATGGAGA
GCTAGACCAAAGCATATAGCAGACTTTGGATCCACCACACGACCTTAACTTTGGCTATCCAAGAC
AATGAATAATTAATTATAAGCGTTGAGTTGCCAATATATTAGCTAGTTATATTAACTCG
Found at i:12266890 original size:18 final size:19
Alignment explanation
Indices: 12266867--12266902 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12266857 TTTTCTTATT
*
12266867 TATATT-ATTATTTTTTAA
1 TATATTAATTAATTTTTAA
12266885 TATATTAATTAATTTTTA
1 TATATTAATTAATTTTTA
12266903 TTTATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTAATTAATTTTTAA
Found at i:12267123 original size:17 final size:17
Alignment explanation
Indices: 12267079--12267133 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
12267069 TTTTTATCAA
*
12267079 TATTATTATTATAAAGTTT
1 TATTA-TATTTTAAA-TTT
*
12267098 TATTAT-TTTT-CATTT
1 TATTATATTTTAAATTT
12267113 TATTATATTTTAAATTT
1 TATTATATTTTAAATTT
12267130 TATT
1 TATT
12267134 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 11 0.35
18 1 0.03
19 5 0.16
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATATTTTAAATTT
Found at i:12268293 original size:3 final size:3
Alignment explanation
Indices: 12268287--12268335 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
12268277 TCTTCTTTTA
** *
12268287 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAA ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12268335 A
1 A
12268336 AATTGAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12271771 original size:28 final size:28
Alignment explanation
Indices: 12271736--12271821 Score: 163
Period size: 28 Copynumber: 3.1 Consensus size: 28
12271726 CTTTTAACTT
*
12271736 AACCAATTTCTTTGTTTTGTTTATTATA
1 AACCAATTTCTTTGTTTTATTTATTATA
12271764 AACCAATTTCTTTGTTTTATTTATTATA
1 AACCAATTTCTTTGTTTTATTTATTATA
12271792 AACCAATTTCTTTGTTTTATTTATTATA
1 AACCAATTTCTTTGTTTTATTTATTATA
12271820 AA
1 AA
12271822 TTACTACCCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (28 bp):
AACCAATTTCTTTGTTTTATTTATTATA
Found at i:12275066 original size:19 final size:21
Alignment explanation
Indices: 12275034--12275074 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12275024 TTAATATTAG
*
12275034 AAAAAAATTCAAG-AAAAGGA
1 AAAAAAAATCAAGAAAAAGGA
12275054 AAAAAAAAT-AAGAAAAAGGA
1 AAAAAAAATCAAGAAAAAGGA
12275074 A
1 A
12275075 TAGTGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (21 bp):
AAAAAAAATCAAGAAAAAGGA
Found at i:12275194 original size:58 final size:59
Alignment explanation
Indices: 12275125--12275236 Score: 185
Period size: 58 Copynumber: 1.9 Consensus size: 59
12275115 AATTGAAAGC
12275125 TTTTATTTTAAGGAAAATTGATACTTTCAACTTTT-TTCCAA-AA-ATATTTTTTGAAAA
1 TTTTATTTTAAGGAAAATTGATACTTTCAACTTTTCTT-CAAGAATATATTTTTTGAAAA
12275182 TTTTATCTTTAAGGAAAATTGATACTTTCAACTTTTCTTCAAGAATATATTTTTT
1 TTTTAT-TTTAAGGAAAATTGATACTTTCAACTTTTCTTCAAGAATATATTTTTT
12275237 TGTTTTTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
57 6 0.12
58 32 0.63
59 4 0.08
60 9 0.18
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (59 bp):
TTTTATTTTAAGGAAAATTGATACTTTCAACTTTTCTTCAAGAATATATTTTTTGAAAA
Found at i:12275285 original size:11 final size:11
Alignment explanation
Indices: 12275271--12275300 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
12275261 AAAAATCATA
12275271 AAAAATAAAAT
1 AAAAATAAAAT
12275282 AAAAATAAAAT
1 AAAAATAAAAT
12275293 AGAAAATA
1 A-AAAATA
12275301 CCAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:12275327 original size:4 final size:4
Alignment explanation
Indices: 12275318--12275362 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
12275308 ATTCTATTCT
12275318 AATA AATA AAT- AAT- AAT- AAT- AAT- AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
12275361 AA
1 AA
12275363 AACCTTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 15 0.38
4 25 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:12276131 original size:13 final size:13
Alignment explanation
Indices: 12276113--12276137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12276103 ATAAATAAAA
12276113 AATAAAAAATATC
1 AATAAAAAATATC
12276126 AATAAAAAATAT
1 AATAAAAAATAT
12276138 ATATATATAT
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAAATATC
Found at i:12276162 original size:8 final size:7
Alignment explanation
Indices: 12276151--12276312 Score: 55
Period size: 8 Copynumber: 21.7 Consensus size: 7
12276141 TATATATACT
12276151 AATAGATA
1 AATA-ATA
12276159 AATAATA
1 AATAATA
12276166 AA-AATA
1 AATAATA
*
12276172 GATAATA
1 AATAATA
**
12276179 GTTAAT-
1 AATAATA
12276185 AATAA-A
1 AATAATA
*
12276191 AAT-TTA
1 AATAATA
* *
12276197 TATACATT
1 AATA-ATA
12276205 AATAGATA
1 AATA-ATA
12276213 AATAATA
1 AATAATA
*
12276220 ATATATATT
1 A-ATA-ATA
12276229 AATAGATA
1 AATA-ATA
*
12276237 AATGATAA
1 AATAAT-A
*
12276245 AATATATT
1 AATA-ATA
12276253 AATAGATAA
1 AATA-AT-A
12276262 AATATATA
1 AATA-ATA
*
12276270 TATTAATA
1 -AATAATA
12276278 AATAAT-
1 AATAATA
12276284 AATAATA
1 AATAATA
*
12276291 ATAGCAATA
1 A-A-TAATA
12276300 AATAAATA
1 AAT-AATA
12276308 AATAA
1 AATAA
12276313 GATATAAAAT
Statistics
Matches: 115, Mismatches: 24, Indels: 31
0.68 0.14 0.18
Matches are distributed among these distances:
6 20 0.17
7 28 0.24
8 48 0.42
9 19 0.17
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (7 bp):
AATAATA
Found at i:12276169 original size:78 final size:77
Alignment explanation
Indices: 12276087--12276262 Score: 187
Period size: 78 Copynumber: 2.3 Consensus size: 77
12276077 ATCACAGCAA
* *
12276087 AAAAAAATATTAATAGATAAATAAAAAATAAAAAATATCAATA-AAAAATATATATATATATACT
1 AAAAATATATTAATAGATAAATAAAAAATAAAAAACATCAATAGAAAAATA-ATA-ATATATACT
12276151 AATAGATAAATAAT
64 AATAGATAAATAAT
* * * * * * * * *
12276165 AAAAATAGA-TAATAGTTAATAATAAAAATTTATATACATTAATAGATAAATAATAATATATATT
1 AAAAATATATTAATAGAT-A-AATAAAAAATAAAAAACATCAATAGAAAAATAATAATATATACT
*
12276229 AATAGATAAATGAT
64 AATAGATAAATAAT
12276243 -AAAATATATTAATAGATAAA
1 AAAAATATATTAATAGATAAA
12276263 ATATATATAT
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
76 2 0.03
77 15 0.19
78 36 0.45
79 21 0.26
80 6 0.08
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (77 bp):
AAAAATATATTAATAGATAAATAAAAAATAAAAAACATCAATAGAAAAATAATAATATATACTAA
TAGATAAATAAT
Found at i:12276188 original size:17 final size:17
Alignment explanation
Indices: 12276092--12276290 Score: 71
Period size: 17 Copynumber: 11.6 Consensus size: 17
12276082 AGCAAAAAAA
*
12276092 AATATTAATAGATAAAT
1 AATAATAATAGATAAAT
* *
12276109 AA-AA-AATAAAAAATAT
1 AATAATAATAGATAA-AT
* * *
12276125 CAATAAAAAATATATATAT
1 -AAT-AATAATAGATAAAT
*
12276144 ATATACTAATAGATAAAT
1 A-ATAATAATAGATAAAT
*
12276162 AATAAAAATAGAT-AAT
1 AATAATAATAGATAAAT
*
12276178 AGTTAATAATA-A-AAATTT
1 A-ATAATAATAGATAAA--T
12276196 ATATACATTAATAGATAAAT
1 A-ATA-A-TAATAGATAAAT
* *
12276216 AATAAT-ATATATTAAT
1 AATAATAATAGATAAAT
12276232 AGAT-A-AAT-GATAAA-
1 A-ATAATAATAGATAAAT
*
12276246 ATATATTAATAGATAAA-
1 A-ATAATAATAGATAAAT
*
12276263 ATATATATATTA-ATAAAT
1 A-ATA-ATAATAGATAAAT
12276281 AATAATAATA
1 AATAATAATA
12276291 ATAGCAATAA
Statistics
Matches: 136, Mismatches: 25, Indels: 43
0.67 0.12 0.21
Matches are distributed among these distances:
14 3 0.02
15 11 0.08
16 30 0.22
17 43 0.32
18 22 0.16
19 10 0.07
20 13 0.10
21 1 0.01
22 3 0.02
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AATAATAATAGATAAAT
Found at i:12276213 original size:24 final size:24
Alignment explanation
Indices: 12276180--12276290 Score: 108
Period size: 24 Copynumber: 4.8 Consensus size: 24
12276170 TAGATAATAG
*
12276180 TTAATA-ATAAA-AATTTATATACA
1 TTAATAGATAAATAA-TAATATACA
*
12276203 TTAATAGATAAATAATAATATATA
1 TTAATAGATAAATAATAATATACA
* * *
12276227 TTAATAGATAAATGATAAAATATA
1 TTAATAGATAAATAATAATATACA
*
12276251 TTAATAGAT-AA-AAT-ATATATA
1 TTAATAGATAAATAATAATATACA
*
12276272 TTAATAAAT-AATAATAATA
1 TTAATAGATAAATAATAATA
12276291 ATAGCAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
21 16 0.21
22 5 0.06
23 11 0.14
24 43 0.56
25 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (24 bp):
TTAATAGATAAATAATAATATACA
Found at i:12276232 original size:54 final size:55
Alignment explanation
Indices: 12276095--12276290 Score: 154
Period size: 54 Copynumber: 3.5 Consensus size: 55
12276085 AAAAAAAAAT
* * *
12276095 ATTAATAGATAAATAAAAAATA-AAAAATA-TCAATAAAAAATATATATATATAT
1 ATTAATAGATAAATAATAAATATAATAATAGTCAATAAAAAATATATATATATAC
* * *
12276148 ACTAATAGATAAATAATAAAAATAGATAATAGTTAATAATAAAA-AT-T-TATATAC
1 ATTAATAGATAAATAATAAATATA-ATAATAGTCAATAA-AAAATATATATATATAC
* * * *
12276202 ATTAATAGATAAATAATAATATATATTAATAGATAAATGATAAAATATAT-TA-ATAG
1 ATTAATAGATAAATAATAA-ATATAATAATAG-TCAAT-AAAAAATATATATATATAC
* * *
12276258 ATAAAATATATATATTAATAAATAATAATAATA
1 AT-TAATAGATA-AATAATAAAT-ATAATAATA
12276291 ATAGCAATAA
Statistics
Matches: 115, Mismatches: 16, Indels: 19
0.77 0.11 0.13
Matches are distributed among these distances:
53 19 0.17
54 31 0.27
55 18 0.16
56 16 0.14
57 16 0.14
58 15 0.13
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (55 bp):
ATTAATAGATAAATAATAAATATAATAATAGTCAATAAAAAATATATATATATAC
Found at i:12276267 original size:41 final size:41
Alignment explanation
Indices: 12276204--12276290 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
12276194 TTATATACAT
* * * *
12276204 TAATAGATAAATAATAATATATAT-TAATAGATAAATGATAA
1 TAATATATTAATAATAAAATATATATAATA-ATAAATAATAA
*
12276245 -AATATATTAATAGATAAAATATATATATTAATAAATAATAA
1 TAATATATTAATA-ATAAAATATATATAATAATAAATAATAA
12276286 TAATA
1 TAATA
12276291 ATAGCAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
40 10 0.26
41 20 0.53
42 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (41 bp):
TAATATATTAATAATAAAATATATATAATAATAAATAATAA
Found at i:12276498 original size:13 final size:13
Alignment explanation
Indices: 12276477--12276506 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12276467 CACTCGACTC
*
12276477 TTTTCTTTTTTTT
1 TTTTATTTTTTTT
12276490 TTTTATTTTTTTT
1 TTTTATTTTTTTT
12276503 TTTT
1 TTTT
12276507 GGTTGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTATTTTTTTT
Found at i:12276662 original size:42 final size:43
Alignment explanation
Indices: 12276525--12276700 Score: 200
Period size: 42 Copynumber: 4.1 Consensus size: 43
12276515 TTTTGATTAA
*
12276525 GCTCCTCTAAACAGAGGCTCAAC-G-AC-TTTGTAAAAATAAATT
1 GCTCCTCTAAACAGAGG--CAACAGAACTTTTGAAAAAATAAATT
* * *
12276567 GCTCATCTAAATAGAGGCAACATAACTACTTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACA-GA--ACTTTTGAAAAAATAAATT
* *
12276613 GCTCCTCTAAACAGGGGCAACAGAACTTTTG-AAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACAGAACTTTTGAAAAAATAAATT
* *
12276655 GCTCCTCTAAACAGAGGCACCACAA-TTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACAGAACTTTTGAAAAAATAAATT
12276697 GCTC
1 GCTC
12276701 ATTGACAATC
Statistics
Matches: 114, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
40 4 0.04
41 5 0.04
42 61 0.54
43 7 0.06
45 3 0.03
46 34 0.30
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (43 bp):
GCTCCTCTAAACAGAGGCAACAGAACTTTTGAAAAAATAAATT
Found at i:12277734 original size:7 final size:7
Alignment explanation
Indices: 12277722--12277754 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
12277712 TCCTCTTTTT
12277722 TTTTTCA
1 TTTTTCA
12277729 TTTTTCA
1 TTTTTCA
*
12277736 TTTTTTA
1 TTTTTCA
12277743 TTTTTCA
1 TTTTTCA
12277750 TTTTT
1 TTTTT
12277755 TTTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:12277741 original size:16 final size:15
Alignment explanation
Indices: 12277720--12277773 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
12277710 AGTCCTCTTT
12277720 TTTTTTTCATTTTTCA
1 TTTTTTT-ATTTTTCA
12277736 -TTTTTTATTTTTCA
1 TTTTTTTATTTTTCA
*
12277750 TTTTTTTTATTATTTTA
1 -TTTTTTTATT-TTTCA
12277767 TTTTTTT
1 TTTTTTT
12277774 TAAGCATAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 16 0.47
17 4 0.12
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:12277745 original size:14 final size:15
Alignment explanation
Indices: 12277721--12277755 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
12277711 GTCCTCTTTT
12277721 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
12277736 TTTTTT-ATTTTTCA
1 TTTTTTCATTTTTCA
12277750 TTTTTT
1 TTTTTT
12277756 TTATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:12277772 original size:7 final size:7
Alignment explanation
Indices: 12277717--12277772 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
12277707 TTGAGTCCTC
12277717 TTTTT-T
1 TTTTTAT
*
12277723 TTTTCAT
1 TTTTTAT
*
12277730 TTTTCAT
1 TTTTTAT
12277737 TTTTTAT
1 TTTTTAT
*
12277744 TTTTCATTT
1 TTTT--TAT
12277753 TTTTTAT
1 TTTTTAT
12277760 TATTTTAT
1 T-TTTTAT
12277768 TTTTT
1 TTTTT
12277773 TTAAGCATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
6 4 0.10
7 25 0.60
8 7 0.17
9 6 0.14
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:12277775 original size:17 final size:16
Alignment explanation
Indices: 12277719--12277775 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
12277709 GAGTCCTCTT
12277719 TTTTTTTTCATTTTTCA
1 TTTTTTTT-ATTTTTCA
12277736 --TTTTTTATTTTTCA
1 TTTTTTTTATTTTTCA
*
12277750 TTTTTTTTATTATTTTA
1 TTTTTTTTATT-TTTCA
12277767 TTTTTTTTA
1 TTTTTTTTA
12277776 AGCATAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 8 0.22
15 6 0.17
16 9 0.25
17 13 0.36
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTATTTTTCA
Found at i:12288187 original size:18 final size:21
Alignment explanation
Indices: 12288154--12288195 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
12288144 TTTAATATTA
12288154 GAAAAAAAATTCAAG-AAAAG
1 GAAAAAAAATTCAAGAAAAAG
12288174 GAAAAAAAA-T-AAGAAAAAG
1 GAAAAAAAATTCAAGAAAAAG
12288193 GAA
1 GAA
12288196 TAGTGATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (21 bp):
GAAAAAAAATTCAAGAAAAAG
Found at i:12288327 original size:60 final size:60
Alignment explanation
Indices: 12288249--12288428 Score: 303
Period size: 59 Copynumber: 3.0 Consensus size: 60
12288239 ACATGAAAGC
*
12288249 TTTTA-TTTTAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAATT
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATT
12288308 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA-T
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATT
* *
12288367 TTTGATTTTTAAGGAAAATTGATACTTTCAAC-TTTTCGTCAAGAATATTTTTTTGAAATT
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTTGAAATT
12288427 TT
1 TT
12288429 ATTTTGGAAA
Statistics
Matches: 115, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
58 5 0.04
59 56 0.49
60 54 0.47
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (60 bp):
TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATT
Found at i:12288461 original size:12 final size:12
Alignment explanation
Indices: 12288446--12288476 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
12288436 AAAATTCATA
12288446 AAAAAATAAAAT
1 AAAAAATAAAAT
12288458 -AAAAATAAAAT
1 AAAAAATAAAAT
12288469 AAAAAATA
1 AAAAAATA
12288477 CTAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Done.