Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_pilon, 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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 11 of 12
Found at i:2654526 original size:7 final size:7
Alignment explanation
Indices: 2654514--2654543 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2654504 GGTTAGCTAC
2654514 CATTTGA
1 CATTTGA
2654521 CATTTGA
1 CATTTGA
2654528 CATTTGA
1 CATTTGA
2654535 CATTTGA
1 CATTTGA
2654542 CA
1 CA
2654544 ATATTCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (7 bp):
CATTTGA
Found at i:2663036 original size:17 final size:17
Alignment explanation
Indices: 2663014--2663052 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2663004 AATGAACCGC
2663014 GCGTGGATAGACTCCTT
1 GCGTGGATAGACTCCTT
2663031 GCGTGGATAGACTCCTT
1 GCGTGGATAGACTCCTT
2663048 G-GTGG
1 GCGTGG
2663053 TTCGGGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.15, C:0.21, G:0.36, T:0.28
Consensus pattern (17 bp):
GCGTGGATAGACTCCTT
Found at i:2664114 original size:12 final size:10
Alignment explanation
Indices: 2664084--2664112 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2664074 TATTCTCTTT
2664084 AATTCTCTCA
1 AATTCTCTCA
2664094 AATTCTCTCA
1 AATTCTCTCA
2664104 AATTCTCTC
1 AATTCTCTC
2664113 TCTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTCTCTCA
Found at i:2665898 original size:18 final size:18
Alignment explanation
Indices: 2665875--2665912 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2665865 ACAGCATCCA
*
2665875 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
2665893 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2665911 CC
1 CC
2665913 ACCGCCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:2666563 original size:38 final size:34
Alignment explanation
Indices: 2666512--2666594 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 34
2666502 TTCAGTTAAT
2666512 TTTGTT-TA-TTACCATTTAATATCCGTTATTGTAA-
1 TTTGTTATATTTACCATTTAAT-T-C-TTATTGTAAG
2666546 TTTGGTTATCATTTACCATTTAATTCTTATTGTAAG
1 TTT-GTTAT-ATTTACCATTTAATTCTTATTGTAAG
2666582 TTTGTTATATTTA
1 TTTGTTATATTTA
2666595 AAATTATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
34 8 0.18
35 17 0.39
36 5 0.11
37 2 0.05
38 12 0.27
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (34 bp):
TTTGTTATATTTACCATTTAATTCTTATTGTAAG
Found at i:2673648 original size:35 final size:30
Alignment explanation
Indices: 2673605--2673671 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 30
2673595 AAAAAACACA
2673605 ATATATCGTTATTTTCGTTTTTTATTTAATTAAG
1 ATATATCG-T-TTTT-G-TTTTTATTTAATTAAG
2673639 ATATGATCGTTTTTGTTTTTATTTAATTAAG
1 ATAT-ATCGTTTTTGTTTTTATTTAATTAAG
2673670 AT
1 AT
2673672 GTAATCGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 18 0.56
32 1 0.03
33 4 0.12
34 5 0.16
35 4 0.12
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.58
Consensus pattern (30 bp):
ATATATCGTTTTTGTTTTTATTTAATTAAG
Found at i:2673987 original size:27 final size:25
Alignment explanation
Indices: 2673910--2674024 Score: 78
Period size: 25 Copynumber: 4.4 Consensus size: 25
2673900 TTAAACTCAT
*
2673910 AATATTTTA-TA-TATATTAATTAAAA
1 AATATTTTATTATTA-ATTTATT-AAA
* *
2673935 AATATATTTTTATATTAACTTATTAAA
1 AATAT-TTTAT-TATTAATTTATTAAA
2673962 TAA-ATTTTATTATTAATTTAATTTAAA
1 -AATATTTTATTATTAATTT-A-TTAAA
*
2673989 AATATTTTATT-TTAATTT-TAAAA
1 AATATTTTATTATTAATTTATTAAA
2674012 TATATATTTTATT
1 -A-ATATTTTATT
2674025 CTTATCTAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
23 4 0.05
24 1 0.01
25 23 0.31
26 17 0.23
27 18 0.24
28 9 0.12
29 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTTTATTATTAATTTATTAAA
Found at i:2674019 original size:20 final size:21
Alignment explanation
Indices: 2673969--2674022 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2673959 AAATAAATTT
*
2673969 TATTATTAATTTAATTTAAAAA
1 TATTA-TATTTTAATTTAAAAA
* *
2673991 TATTTTATTTTAATTTTAAAA
1 TATTATATTTTAATTTAAAAA
2674012 TA-TATATTTTA
1 TATTATATTTTA
2674023 TTCTTATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 8 0.29
21 16 0.57
22 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATATTTTAATTTAAAAA
Found at i:2674451 original size:27 final size:26
Alignment explanation
Indices: 2674377--2674461 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
2674367 TAATAGACAT
*
2674377 TTATAATAATTAATCTT-AATTAATTAA
1 TTATAA-AATTAAT-TTCAAATAATTAA
* * *
2674404 TTAATATATTTAATATC-AATAATTGAA
1 TT-ATAAAATTAATTTCAAATAATT-AA
2674431 TTATAAAATTAATTTCAAATAA-TAA
1 TTATAAAATTAATTTCAAATAATTAA
2674456 TT-TAAA
1 TTATAAA
2674462 TCTAAAAACT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
24 4 0.09
25 4 0.09
26 19 0.40
27 17 0.36
28 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (26 bp):
TTATAAAATTAATTTCAAATAATTAA
Found at i:2676824 original size:44 final size:44
Alignment explanation
Indices: 2676768--2676857 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
2676758 TGTTGGGGAC
*
2676768 TTGGGTCCTTGTGACGTTAACAGCATTATGTAATTATGGACTGA
1 TTGGGTCCTTGTGACGTTAACAGCATTATGTAATTATGAACTGA
*
2676812 TTGGGTCCTTGTGATGTTAACAGCATTATGTAATTATGAACTGA
1 TTGGGTCCTTGTGACGTTAACAGCATTATGTAATTATGAACTGA
2676856 TT
1 TT
2676858 TCTAGAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (44 bp):
TTGGGTCCTTGTGACGTTAACAGCATTATGTAATTATGAACTGA
Found at i:2681505 original size:15 final size:15
Alignment explanation
Indices: 2681465--2681506 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2681455 GATTACTCTT
* *
2681465 TTTAAATAATTTGAA
1 TTTAAATCATTTCAA
2681480 TTTATAA-CATTTCAA
1 TTTA-AATCATTTCAA
2681495 TTTAAATCATTT
1 TTTAAATCATTT
2681507 ATCGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTAAATCATTTCAA
Found at i:2693825 original size:2 final size:2
Alignment explanation
Indices: 2693813--2693880 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
2693803 TTTGGGGTAT
*
2693813 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2693855 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
2693881 AGGATAGGGC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2697569 original size:20 final size:19
Alignment explanation
Indices: 2697544--2697588 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2697534 CATTTCCTTG
*
2697544 CTTTCTTCTGCTCTTTTTCT
1 CTTTCTTCTGCACTTTTT-T
*
2697564 CTTTC-TCTTCACTTTTTT
1 CTTTCTTCTGCACTTTTTT
2697582 CTTTCTT
1 CTTTCTT
2697589 TCAGATTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (19 bp):
CTTTCTTCTGCACTTTTTT
Found at i:2697584 original size:18 final size:18
Alignment explanation
Indices: 2697556--2697591 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2697546 TTCTTCTGCT
2697556 CTTTTTCTCTTTCTCTTCA
1 CTTTTTCTCTTTCT-TTCA
2697575 CTTTTT-TCTTTCTTTCA
1 CTTTTTCTCTTTCTTTCA
2697592 GATTGGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCA
Found at i:2701324 original size:42 final size:42
Alignment explanation
Indices: 2701276--2701393 Score: 209
Period size: 42 Copynumber: 2.8 Consensus size: 42
2701266 CCCTGAATTC
*
2701276 CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
1 CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTT
* *
2701318 TCCGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAACGTTTT
1 CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTT
2701360 CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2701394 TGTAATTCAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
CCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTT
Found at i:2701609 original size:10 final size:9
Alignment explanation
Indices: 2701594--2701645 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 9
2701584 TATTTAAAAT
2701594 ATATTTATTA
1 ATATTTA-TA
2701604 ATATTTATA
1 ATATTTATA
2701613 ATAATATAATATA
1 AT-AT-T--TATA
2701626 ATATTTATA
1 ATATTTATA
2701635 ATATTATATA
1 ATATT-TATA
2701645 A
1 A
2701646 AATAATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 13 0.35
10 14 0.38
11 2 0.05
12 2 0.05
13 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATTTATA
Found at i:2701627 original size:22 final size:22
Alignment explanation
Indices: 2701602--2701682 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
2701592 ATATATTTAT
2701602 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
*
2701624 TAATATTTATAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
2701648 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
2701671 TAAGATATTATA
1 TAATAT-TTATA
2701683 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
22 17 0.36
23 12 0.26
24 13 0.28
25 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:2702132 original size:15 final size:15
Alignment explanation
Indices: 2702112--2702147 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2702102 CATTTTCTAG
2702112 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
2702127 AATTCAAATTTGAGT
1 AATTCAAATTCCAGT
2702142 AATTCA
1 AATTCA
2702148 TTTTCTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:2717104 original size:114 final size:113
Alignment explanation
Indices: 2716906--2717224 Score: 408
Period size: 114 Copynumber: 2.8 Consensus size: 113
2716896 GTCCATGACA
* * * * *
2716906 AGTGCGGCAGTTTTGTCCACGTCGACCAGAG-ACTGCATCCGTATTTTCTTTGTGGAGGTTCAGG
1 AGTGCGGCAGTTGTGTCCACGTCGACCACAGTACTGCATCGGTATTTTCCTTGTGGAGGTTTAGG
*
2716970 GACCATTGGCTGGGGATTCCCTTCTTCCGTAGTCTGACAGAAAACAAC
66 GACCATTGGCTGGGGATTCCCTTCTTCCGTAATCTGACAGAAAACAAC
* * * * *
2717018 AGTGCGGCGGTTGTGTCCACATCGACCACAGCTACCGCATCGGTATTTTCCATGTGGAAGTTTAG
1 AGTGCGGCAGTTGTGTCCACGTCGACCACAG-TACTGCATCGGTATTTTCCTTGTGGAGGTTTAG
* *
2717083 GGACCATTGGCTGGGGATTCCCTCCTTCTGTAATCTGACAGAAAACAAC
65 GGACCATTGGCTGGGGATTCCCTTCTTCCGTAATCTGACAGAAAACAAC
* * ** * *
2717132 AGAGCGGCAGTTGTGTCC-CTGTCGACCACAGTGACTGCATTGGTATTTTTGTTGTGGAGGCTTC
1 AGTGCGGCAGTTGTGTCCAC-GTCGACCACAGT-ACTGCATCGGTATTTTCCTTGTGGAGGTTTA
**
2717196 CAGACCATTGGCTGGGGATTCCCTTCTTC
64 GGGACCATTGGCTGGGGATTCCCTTCTTC
2717225 TGCAACCTGG
Statistics
Matches: 176, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
112 27 0.15
113 2 0.01
114 147 0.84
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (113 bp):
AGTGCGGCAGTTGTGTCCACGTCGACCACAGTACTGCATCGGTATTTTCCTTGTGGAGGTTTAGG
GACCATTGGCTGGGGATTCCCTTCTTCCGTAATCTGACAGAAAACAAC
Found at i:2717537 original size:45 final size:45
Alignment explanation
Indices: 2717436--2717523 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
2717426 CACAGTTGCT
* *
2717436 CTCTCCAGAGATCAGAATGTTCCAGACTTACTGGAGGAGCTGGCA
1 CTCTCCAGAGATCAGGATGTTCCAGACTTACCGGAGGAGCTGGCA
2717481 CTCTCCAGAGATCAGGATGTTCC-GAACTTACCGGAGGAGCTGG
1 CTCTCCAGAGATCAGGATGTTCCAG-ACTTACCGGAGGAGCTGG
2717524 ATCTTGCTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (45 bp):
CTCTCCAGAGATCAGGATGTTCCAGACTTACCGGAGGAGCTGGCA
Found at i:2719547 original size:22 final size:20
Alignment explanation
Indices: 2719488--2719552 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 20
2719478 TATATATATC
2719488 TTTAATTATA-TTTTTTTTA
1 TTTAATTATACTTTTTTTTA
*
2719507 TTTAATATATTCCTTTTTTTTTA
1 TTTAAT-TA-TAC-TTTTTTTTA
*
2719530 TTTATATTATACTATTTTTTA
1 TTTA-ATTATACTTTTTTTTA
2719551 TT
1 TT
2719553 ATATATATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 11 0.29
22 2 0.05
23 15 0.39
24 2 0.05
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTAATTATACTTTTTTTTA
Found at i:2719547 original size:24 final size:25
Alignment explanation
Indices: 2719498--2719560 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2719488 TTTAATTATA
* *
2719498 TTTTTTTTATTTA-A-TATATTCCT
1 TTTTTTTTATTTATATTATACTCAT
2719521 TTTTTTTTATTTATATTATACT-AT
1 TTTTTTTTATTTATATTATACTCAT
* *
2719545 TTTTTATTATATATAT
1 TTTTTTTTATTTATAT
2719561 CTTATATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.38
24 16 0.47
25 5 0.15
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTTATTTATATTATACTCAT
Found at i:2719557 original size:2 final size:2
Alignment explanation
Indices: 2719552--2719595 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
2719542 TATTTTTTAT
*
2719552 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
2719593 TA T
1 TA T
2719596 GTATTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2719706 original size:2 final size:2
Alignment explanation
Indices: 2719699--2719728 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2719689 TTTATTTATT
2719699 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2719729 TTTTACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2719710 original size:40 final size:42
Alignment explanation
Indices: 2719612--2719711 Score: 111
Period size: 39 Copynumber: 2.5 Consensus size: 42
2719602 ATTTTTCTCC
* *
2719612 ATTTA-TTATGTATATACATTTTTCCTTAATATTATATTTTAT
1 ATTTATTTATATATATATA-TTTTCCTTAATATTATATTTTAT
** *
2719654 ACGT-TTT-TATATATATATTTT-CTTAATATTCTATTTT-T
1 ATTTATTTATATATATATATTTTCCTTAATATTATATTTTAT
2719692 ATTTATTTATATATATATAT
1 ATTTATTTATATATATATAT
2719712 ATATATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
38 3 0.06
39 18 0.38
40 15 0.31
41 8 0.17
42 4 0.08
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (42 bp):
ATTTATTTATATATATATATTTTCCTTAATATTATATTTTAT
Found at i:2719749 original size:18 final size:18
Alignment explanation
Indices: 2719723--2719760 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2719713 TATATATATA
2719723 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
*
2719741 TTATTTTTTTCTATTATT
1 TTATATTTTTCTATTATT
2719759 TT
1 TT
2719761 TTTCTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:2719757 original size:13 final size:13
Alignment explanation
Indices: 2719741--2719765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2719731 TTACTTTATT
2719741 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2719754 TTATTTTTTTCT
1 TTATTTTTTTCT
2719766 TAATATCATG
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2719984 original size:9 final size:9
Alignment explanation
Indices: 2719953--2719990 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2719943 TTTTTTAACA
2719953 TTTTATTCAT
1 TTTTATT-AT
2719963 TTTGT-TTAT
1 TTT-TATTAT
2719972 TTTTATTAT
1 TTTTATTAT
2719981 TTTTATTAT
1 TTTTATTAT
2719990 T
1 T
2719991 ATTTTTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.04
9 19 0.73
10 5 0.19
11 1 0.04
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2723148 original size:7 final size:7
Alignment explanation
Indices: 2723138--2723198 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
2723128 ATAAAAAGAT
2723138 AAAAAAG
1 AAAAAAG
2723145 AAAAAA-
1 AAAAAAG
*
2723151 AACAAAG
1 AAAAAAG
* *
2723158 AGAAAAT
1 AAAAAAG
2723165 AAAAAAG
1 AAAAAAG
2723172 AAAAAAGG
1 AAAAAA-G
2723180 AAAATTGAAG
1 AAAA---AAG
2723190 AAAAAAG
1 AAAAAAG
2723197 AA
1 AA
2723199 GACAAGATGC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.12
7 26 0.60
8 5 0.12
10 5 0.12
11 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:2723163 original size:14 final size:12
Alignment explanation
Indices: 2723138--2723177 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
2723128 ATAAAAAGAT
2723138 AAAAAAGAAAAA
1 AAAAAAGAAAAA
2723150 AAACAAAGAGAAAA
1 AAA-AAAGA-AAAA
2723164 TAAAAAAGAAAAA
1 -AAAAAAGAAAAA
2723177 A
1 A
2723178 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 9 0.36
14 9 0.36
15 3 0.12
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:2723168 original size:20 final size:20
Alignment explanation
Indices: 2723140--2723184 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2723130 AAAAAGATAA
* *
2723140 AAAAGAAAAAA-AACAAAGAG
1 AAAATAAAAAAGAAAAAAG-G
2723160 AAAATAAAAAAGAAAAAAGG
1 AAAATAAAAAAGAAAAAAGG
2723180 AAAAT
1 AAAAT
2723185 TGAAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAATAAAAAAGAAAAAAGG
Found at i:2723379 original size:69 final size:69
Alignment explanation
Indices: 2723256--2723393 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
2723246 GATTTAAACT
2723256 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTTCACTAGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTTCACTAGAAGATCATAGAGCA
2723321 TCAA
66 TCAA
** * * * * *
2723325 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGCATCA-TTCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTTC-ACTAGAAGATCATAGAGC
2723389 ATCAA
65 ATCAA
2723394 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 3 0.05
69 58 0.95
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTTCACTAGAAGATCATAGAGCA
TCAA
Found at i:2724401 original size:32 final size:32
Alignment explanation
Indices: 2724319--2724406 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
2724309 GGAACAATGA
* *
2724319 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATATTG
* * * *
2724351 GGGTATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATATTG
2724383 GGGCATCTTTGG-GAATTCAACATC
1 GGGCATCTTTGGAG-ATTCAACATC
2724407 CTGATGCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 45 0.98
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATATTG
Found at i:2725104 original size:106 final size:106
Alignment explanation
Indices: 2724982--2725197 Score: 315
Period size: 106 Copynumber: 2.0 Consensus size: 106
2724972 ATATCGTGCC
* *
2724982 ACTCGAGACAACACAAGTTCAACTCCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTCCACAGCGAAGGGACGGCTGGCTGTCAACAAACAATTTCCC
*
2725047 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
* * * **
2725088 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGCTCAACTCCACAGCGAAGGGACGGCTGGCTGTCAACAAACAATTTCCC
* * * **
2725153 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
2725194 ACTC
1 ACTC
2725198 AGAACAATAC
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTCCACAGCGAAGGGACGGCTGGCTGTCAACAAACAATTTCCC
AATTCCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
Found at i:2725446 original size:39 final size:38
Alignment explanation
Indices: 2725384--2725503 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 38
2725374 ATGTTTTATA
* * *
2725384 TGAAACAAATTTCATCTC-C-CTTGAGACAGTTTTTTT
1 TGAAACAAATTTCGTCTCTCTCTTGAGACAGTTTCTCT
* * *
2725420 TGGAACTAAGTTTTGTCTCTCTCTTGAGACAGTTTCTCT
1 TGAAAC-AAATTTCGTCTCTCTCTTGAGACAGTTTCTCT
* *
2725459 TGAAACAAATTTCGTCT-T-TCTTGAGACAGTGTCCCT
1 TGAAACAAATTTCGTCTCTCTCTTGAGACAGTTTCTCT
2725495 TGAAACAAA
1 TGAAACAAA
2725504 ATCTTTGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
36 30 0.43
37 10 0.14
38 10 0.14
39 20 0.29
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (38 bp):
TGAAACAAATTTCGTCTCTCTCTTGAGACAGTTTCTCT
Found at i:2725598 original size:67 final size:68
Alignment explanation
Indices: 2725478--2725633 Score: 194
Period size: 67 Copynumber: 2.4 Consensus size: 68
2725468 TTTCGTCTTT
* * **
2725478 CTTGAGACAGTGTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAAC-AAATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAATTTTATC
2725540 TCC
66 TCC
* * *
2725543 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACAAAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAATTTTATC
2725608 TCC
66 TCC
* * *
2725611 ATTGAGACCGTTT-TCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
2725634 ACAGATATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 37 0.47
68 22 0.28
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAATTTTATC
TCC
Found at i:2728038 original size:20 final size:19
Alignment explanation
Indices: 2728015--2728104 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 19
2728005 TATCTTTAAT
2728015 TATATATATTTTTTATTTA
1 TATATATATTTTTTATTTA
*
2728034 CTATAT-TCCTTTTTTTATTTA
1 -TATATAT--ATTTTTTATTTA
2728055 TATTATACTATTTTTTA-TTA
1 TA-TATA-TATTTTTTATTTA
* * *
2728075 TATATATCTTATATCATTATA
1 TATATATATT-TTTTATT-TA
2728096 TATATATAT
1 TATATATAT
2728105 ATGTATTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
18 3 0.05
19 8 0.14
20 13 0.23
21 31 0.55
23 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATATTTTTTATTTA
Found at i:2728068 original size:21 final size:21
Alignment explanation
Indices: 2728017--2728079 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
2728007 TCTTTAATTA
2728017 TATA-TATTTTTTATTTACTA-
1 TATACTATTTTTTATTTA-TAT
*
2728037 TATTCCT-TTTTTTATTTATAT
1 TA-TACTATTTTTTATTTATAT
2728058 TATACTATTTTTTATTATATAT
1 TATACTATTTTTTATT-TATAT
2728080 ATCTTATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 7 0.19
21 23 0.64
22 6 0.17
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
TATACTATTTTTTATTTATAT
Found at i:2728112 original size:19 final size:19
Alignment explanation
Indices: 2728069--2728112 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2728059 ATACTATTTT
*
2728069 TTATTATATATATCTTATA
1 TTATTATATATATCATATA
*
2728088 TCATTATATATAT-ATATA
1 TTATTATATATATCATATA
2728106 TGTATTA
1 T-TATTA
2728113 ATTTTTCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATTATATATATCATATA
Found at i:2728231 original size:44 final size:44
Alignment explanation
Indices: 2728168--2728254 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
2728158 ATTTTATACG
2728168 TTTATATATATATATATTTT-CTTTATATTCTATTTT-TATTTTTA
1 TTTATATATATATATATTTTACTTTAT-TT-TATTTTCTATTTTTA
* *
2728212 TTTATTTATATATATATTTTACTTTATTTTTTTTTCTATTTTT
1 TTTATATATATATATATTTTACTTTATTTTATTTTCTATTTTT
2728255 TTCTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 5 0.13
44 28 0.72
45 6 0.15
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (44 bp):
TTTATATATATATATATTTTACTTTATTTTATTTTCTATTTTTA
Found at i:2728465 original size:19 final size:19
Alignment explanation
Indices: 2728443--2728484 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2728433 TTTTTTAACA
2728443 TTTTATTCATTTTGT-TTAT
1 TTTTATT-ATTTTGTATTAT
*
2728462 TTTTATTATTTTTTATTAT
1 TTTTATTATTTTGTATTAT
2728481 TTTT
1 TTTT
2728485 TACATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTATTTTGTATTAT
Found at i:2728486 original size:10 final size:10
Alignment explanation
Indices: 2728443--2728486 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
2728433 TTTTTTAACA
2728443 TTTTATTCATT
1 TTTTATT-ATT
*
2728454 TTGT-TTA-T
1 TTTTATTATT
2728462 TTTTATTATT
1 TTTTATTATT
2728472 TTTTATTATT
1 TTTTATTATT
2728482 TTTTA
1 TTTTA
2728487 CATGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 18 0.62
11 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTATTATT
Found at i:2732174 original size:21 final size:21
Alignment explanation
Indices: 2732148--2732201 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2732138 TTGCCCATAA
2732148 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGGTGCACTAT
2732169 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGGTGCACTAT
2732190 CATGGTGCATCG
1 CATGGTGCATCG
2732202 ATATCCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.28
Consensus pattern (21 bp):
CATGGTGCATCGGTGCACTAT
Found at i:2732323 original size:21 final size:21
Alignment explanation
Indices: 2732275--2732336 Score: 78
Period size: 17 Copynumber: 3.1 Consensus size: 21
2732265 TGCACAGCAG
*
2732275 GATGCATCGATGCACAATC-T
1 GATGCATCGATGCACAACCTT
2732295 --TG-ATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
2732313 GATGCATCGATGCACAAACCTT
1 GATGCATCGATGCAC-AACCTT
2732335 GA
1 GA
2732337 CGGTGCACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 13 0.36
18 3 0.08
20 2 0.06
21 10 0.28
22 8 0.22
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (21 bp):
GATGCATCGATGCACAACCTT
Found at i:2732357 original size:38 final size:38
Alignment explanation
Indices: 2732275--2732365 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
2732265 TGCACAGCAG
* *
2732275 GATGCATCGATGCACAATCTTGATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTTGATCGATGCACAACCAT
* * *
2732313 GATGCATCGATGCACAAACCTTGA-CGGTGCACTATCAT
1 GATGCATCGATGCAC-AACCTTGATCGATGCACAACCAT
* *
2732351 GGTGCATCGGTGCAC
1 GATGCATCGATGCAC
2732366 TATCATGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 38 0.84
39 7 0.16
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (38 bp):
GATGCATCGATGCACAACCTTGATCGATGCACAACCAT
Found at i:2732363 original size:21 final size:21
Alignment explanation
Indices: 2732337--2732380 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2732327 CAAACCTTGA
2732337 CGGTGCACTATCATGGTGCAT
1 CGGTGCACTATCATGGTGCAT
2732358 CGGTGCACTATCATGGTGCAT
1 CGGTGCACTATCATGGTGCAT
2732379 CG
1 CG
2732381 ATATCCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (21 bp):
CGGTGCACTATCATGGTGCAT
Found at i:2732458 original size:179 final size:181
Alignment explanation
Indices: 2732158--2732518 Score: 683
Period size: 179 Copynumber: 2.0 Consensus size: 181
2732148 CATGGTGCAT
2732158 CGGTGCACTATCATGGTGCATCGGTGCACTATCATGGTGCATCGATATCCTTTCATTAAATTTAA
1 CGGTGCACTATCATGGTGCATCGGTGCACTATCATGGTGCATCGATATCCTTTCATTAAATTTAA
2732223 ATAAACTAGTCGTTACTAGCCATTGCAGCCTTCGTGCATGGATGCACAGCAGGATGCATCGATGC
66 ATAAACTAGTCGTTACTAGCCATTGCAGCCTTCGTGCATGGATGCACAGCAGGATGCATCGATGC
2732288 ACAATC-T-TG-ATCGATGCACAACCTTGATGCATCGATGCACAAACCTTGA
131 ACAATCTTATGCATCGATGCACAACCTTGATGCATCGATGCAC-AACCTTGA
2732337 CGGTGCACTATCATGGTGCATCGGTGCACTATCATGGTGCATCGATATCCTTTCATTAAATTTAA
1 CGGTGCACTATCATGGTGCATCGGTGCACTATCATGGTGCATCGATATCCTTTCATTAAATTTAA
2732402 ATAAACTAGTCGTTACTAGCCATTGCAGCCTTCGTGCATGGATGCACAGCAGGATGCATCGATGC
66 ATAAACTAGTCGTTACTAGCCATTGCAGCCTTCGTGCATGGATGCACAGCAGGATGCATCGATGC
2732467 ACAATCTTGATGCATCGATGCACAACCTTGATGCATCGATGCACAACCTTGA
131 ACAATCTT-ATGCATCGATGCACAACCTTGATGCATCGATGCACAACCTTGA
2732519 TGCATCGATG
Statistics
Matches: 178, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
179 136 0.76
180 1 0.01
182 10 0.06
183 31 0.17
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (181 bp):
CGGTGCACTATCATGGTGCATCGGTGCACTATCATGGTGCATCGATATCCTTTCATTAAATTTAA
ATAAACTAGTCGTTACTAGCCATTGCAGCCTTCGTGCATGGATGCACAGCAGGATGCATCGATGC
ACAATCTTATGCATCGATGCACAACCTTGATGCATCGATGCACAACCTTGA
Found at i:2732480 original size:21 final size:21
Alignment explanation
Indices: 2732454--2732553 Score: 182
Period size: 21 Copynumber: 4.8 Consensus size: 21
2732444 TGCACAGCAG
*
2732454 GATGCATCGATGCACAATCTT
1 GATGCATCGATGCACAACCTT
2732475 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
2732496 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
2732517 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
*
2732538 GATGCATCAATGCACA
1 GATGCATCGATGCACA
2732554 GAAGGATGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (21 bp):
GATGCATCGATGCACAACCTT
Found at i:2732771 original size:29 final size:29
Alignment explanation
Indices: 2732750--2732807 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
2732740 AAACTTTGAA
2732750 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2732779 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2732808 TGACTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2732797 original size:30 final size:30
Alignment explanation
Indices: 2732750--2732809 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
2732740 AAACTTTGAA
2732750 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2732779 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2732810 ACTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2733968 original size:19 final size:20
Alignment explanation
Indices: 2733925--2733972 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2733915 TCTAAATCCT
*
2733925 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
2733945 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
2733964 TTTTCAAAA
1 TTTTCAAAA
2733973 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:2734899 original size:34 final size:32
Alignment explanation
Indices: 2734832--2734901 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2734822 CCTTACAAAC
* * *
2734832 TCCCTAGTTTTTCCGGGCTAAACTAGAAGCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2734864 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2734898 TCCC
1 TCCC
2734902 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2735294 original size:20 final size:20
Alignment explanation
Indices: 2735269--2735343 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
2735259 TGTAGCCTTC
*
2735269 ATGCATGGATGCACAACAGG
1 ATGCATCGATGCACAACAGG
**
2735289 ATGCATCGATGCACAACCTTG
1 ATGCATCGATGCACAA-CAGG
*
2735310 ATGCATCAATGCACAGA-AGG
1 ATGCATCGATGCACA-ACAGG
2735330 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2735344 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 29 0.63
21 16 0.35
22 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAACAGG
Found at i:2735542 original size:29 final size:29
Alignment explanation
Indices: 2735521--2735578 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
2735511 AAACTTTGAA
2735521 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2735550 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2735579 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2735568 original size:30 final size:30
Alignment explanation
Indices: 2735521--2735580 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
2735511 AAACTTTGAA
2735521 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2735550 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2735581 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2742329 original size:2 final size:2
Alignment explanation
Indices: 2742322--2742362 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2742312 GAGTGATTAA
*
2742322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT CT -T 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
2742362 A
1 A
2742363 ATCTTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2742370 original size:10 final size:12
Alignment explanation
Indices: 2742329--2742371 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
2742319 TAAATATATA
*
2742329 TATATATATATAT
1 TATATATA-ATCT
2742342 ATATATATAATCT
1 -TATATATAATCT
2742355 TATATATAATCT
1 TATATATAATCT
2742367 TATAT
1 TATAT
2742372 TGTATAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 3 0.11
14 8 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATAATCT
Found at i:2746088 original size:16 final size:16
Alignment explanation
Indices: 2746067--2746100 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2746057 TTACTATTCA
*
2746067 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2746083 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2746099 CG
1 CG
2746101 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2753818 original size:21 final size:22
Alignment explanation
Indices: 2753773--2753818 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2753763 GAATTTGTTT
*
2753773 AATTGTTATAAAATTATCATTA
1 AATTGTTATAAAATTATCATAA
* *
2753795 AATT-TTATAGAATTATTATAA
1 AATTGTTATAAAATTATCATAA
2753816 AAT
1 AAT
2753819 AATTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTGTTATAAAATTATCATAA
Found at i:2754161 original size:3 final size:3
Alignment explanation
Indices: 2754153--2754181 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2754143 TCCTACCAGA
2754153 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2754182 TAGAGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2754883 original size:30 final size:30
Alignment explanation
Indices: 2754847--2754914 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
2754837 TTAGTTCTTA
2754847 AGCTTCAACTATAAATACCCTAACCCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
*
2754877 AGCTTCAATTATAAATACCCTAACCCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
2754907 AGCTTCAA
1 AGCTTCAA
2754915 AATCATCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAACCCATTT
Found at i:2758268 original size:21 final size:21
Alignment explanation
Indices: 2758242--2758289 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2758232 TATGTTGATG
*
2758242 ACATGCTTGTTGCAGGCTCAA
1 ACATGCTCGTTGCAGGCTCAA
*
2758263 ACATGCTCGTTGTAGGCTCAA
1 ACATGCTCGTTGCAGGCTCAA
2758284 ACATGC
1 ACATGC
2758290 AATAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
ACATGCTCGTTGCAGGCTCAA
Found at i:2770679 original size:21 final size:21
Alignment explanation
Indices: 2770623--2770670 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
2770613 ATACCCTTGA
2770623 TGCATCAGTACACATTGAATG
1 TGCATCAGTACACATTGAATG
2770644 TGCATCAGTACACATTGAATG
1 TGCATCAGTACACATTGAATG
2770665 TGCATC
1 TGCATC
2770671 GATGCACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (21 bp):
TGCATCAGTACACATTGAATG
Found at i:2772856 original size:20 final size:20
Alignment explanation
Indices: 2772831--2772868 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2772821 TTCCCCTTGA
2772831 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
2772851 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
2772869 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:2773071 original size:21 final size:21
Alignment explanation
Indices: 2773047--2773095 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2773037 ATACCCTTGA
2773047 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
*
2773068 TGCATCGGTACATATTGAATG
1 TGCATCGGTACACATTGAATG
2773089 TGCATCG
1 TGCATCG
2773096 ATGCACATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (21 bp):
TGCATCGGTACACATTGAATG
Found at i:2776875 original size:23 final size:23
Alignment explanation
Indices: 2776845--2776888 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2776835 ATTACATATA
2776845 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
2776868 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
2776889 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:2784464 original size:28 final size:29
Alignment explanation
Indices: 2784431--2784486 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2784421 GGTTACTGTA
*
2784431 TTATAAAATAATTATTAA-ATTTATCATT
1 TTATAAAATAATAATTAAGATTTATCATT
* *
2784459 TTATAAAATGATAATTAAGGTTTATCAT
1 TTATAAAATAATAATTAAGATTTATCAT
2784487 AATATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (29 bp):
TTATAAAATAATAATTAAGATTTATCATT
Found at i:2789206 original size:15 final size:15
Alignment explanation
Indices: 2789158--2789206 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
2789148 AAATATTAAT
*
2789158 TATAATATAAATGTTGA
1 TATAATAT-TATG-TGA
2789175 TAT-ATATTATGT-A
1 TATAATATTATGTGA
2789188 -ATAATATTATGTGA
1 TATAATATTATGTGA
2789202 TATAA
1 TATAA
2789207 ATGATACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
12 2 0.07
13 10 0.36
14 2 0.07
15 7 0.25
16 4 0.14
17 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
TATAATATTATGTGA
Found at i:2790671 original size:12 final size:12
Alignment explanation
Indices: 2790656--2790680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2790646 ATAACACTTT
2790656 AAAAAAATATTA
1 AAAAAAATATTA
2790668 AAAAAAATATTA
1 AAAAAAATATTA
2790680 A
1 A
2790681 CATTTCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAAATATTA
Found at i:2793559 original size:15 final size:16
Alignment explanation
Indices: 2793539--2793568 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2793529 TAACTAGTGA
2793539 CCTCTTTCTC-TTTTG
1 CCTCTTTCTCATTTTG
2793554 CCTCTTTCTCATTTT
1 CCTCTTTCTCATTTT
2793569 TTTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.60
Consensus pattern (16 bp):
CCTCTTTCTCATTTTG
Found at i:2799436 original size:36 final size:36
Alignment explanation
Indices: 2799385--2799460 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
2799375 CCAAGCTTAC
*
2799385 TCTCAACTACCGCAAGAGCTTTCGATTCTTCGGGTT
1 TCTCAACTACCGCAAGAGCTTTCGATTCTTCAGGTT
*
2799421 TCTCAACTACTGCAAGAGCTTTCGATTCTTCAGGTT
1 TCTCAACTACCGCAAGAGCTTTCGATTCTTCAGGTT
2799457 TCTC
1 TCTC
2799461 CTCCGTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (36 bp):
TCTCAACTACCGCAAGAGCTTTCGATTCTTCAGGTT
Found at i:2802036 original size:17 final size:17
Alignment explanation
Indices: 2802002--2802055 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
2801992 ACCGAACAAA
* *
2802002 TTTATTATTTTAGAGAG
1 TTTATTAATTTAAAGAG
**
2802019 TTTATTAATTTATCGAG
1 TTTATTAATTTAAAGAG
2802036 --TATTAATTTAAAGAG
1 TTTATTAATTTAAAGAG
2802051 TTTAT
1 TTTAT
2802056 ACTGTAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTAAAGAG
Found at i:2806839 original size:139 final size:141
Alignment explanation
Indices: 2806584--2806842 Score: 389
Period size: 139 Copynumber: 1.9 Consensus size: 141
2806574 TATCCAATGA
* * * *
2806584 GTATAAGATAAGTCCTTATGGATGCAATATGGGGACTACATTATGGTGTACGAGATGAGGGTATT
1 GTATAAGATAAGTCCTTATGGATGCAATATAGGGACTACATTACGGTGTACGAGAGGAGGGTACT
*
2806649 TATGAATTTTAAAATATAAACCTCACTGTTACTTTATGAAATGTTACTGAATTATGGTGTACGAG
66 TATGAATTTTAAAATATAAACCTCAATGTTACTTTATGAAATGTTACTGAATTATGGTGTACGAG
2806714 ACTACATTACG
131 ACTACATTACG
* * * * *
2806725 GTATAGGATAAGTTCTTATGGATGCAGTGTAGGGACTACATTACGGTGTATG-G-GGAGGGTACT
1 GTATAAGATAAGTCCTTATGGATGCAATATAGGGACTACATTACGGTGTACGAGAGGAGGGTACT
*
2806788 TATGAATTTTAAAATATAAACCTCAATGTTACTTTATGAAACT-TTATTGAATTAT
66 TATGAATTTTAAAATATAAACCTCAATGTTACTTTATGAAA-TGTTACTGAATTAT
2806843 TTTCTAAATA
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
139 59 0.56
140 2 0.02
141 45 0.42
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (141 bp):
GTATAAGATAAGTCCTTATGGATGCAATATAGGGACTACATTACGGTGTACGAGAGGAGGGTACT
TATGAATTTTAAAATATAAACCTCAATGTTACTTTATGAAATGTTACTGAATTATGGTGTACGAG
ACTACATTACG
Found at i:2823151 original size:13 final size:13
Alignment explanation
Indices: 2823126--2823163 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2823116 TATAACTCGA
2823126 TATATTATTAAATT
1 TATATT-TTAAATT
2823140 TATATTTTAAATT
1 TATATTTTAAATT
2823153 TATATATTTAA
1 TATAT-TTTAA
2823164 TCAGCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTTTAAATT
Found at i:2830819 original size:20 final size:20
Alignment explanation
Indices: 2830794--2830908 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
2830784 TGCGATATTC
**
2830794 CAAATTCGCAACGCGTTAGT
1 CAAATTCGCAACGCGAAAGT
*
2830814 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
2830834 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * **
2830854 CAAATTCGTAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
* *
2830873 CAAATTCGCAA--CTAAATTT
1 CAAATTCGCAACGCGAAA-GT
2830892 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
2830909 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
18 2 0.03
19 27 0.34
20 47 0.59
21 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2830877 original size:19 final size:19
Alignment explanation
Indices: 2830833--2830899 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2830823 AACGCGAAAG
* **
2830833 TCAAATTCGTAACGCGAAAG
1 TCAAATTCGTAAC-TGAATT
2830853 TCAAATTCGTAACTGAATT
1 TCAAATTCGTAACTGAATT
* *
2830872 TCAAATTCGCAACTAAATT
1 TCAAATTCGTAACTGAATT
2830891 TCAAATTCG
1 TCAAATTCG
2830900 CAACGCGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (19 bp):
TCAAATTCGTAACTGAATT
Found at i:2830900 original size:19 final size:19
Alignment explanation
Indices: 2830853--2830903 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
2830843 AACGCGAAAG
* *
2830853 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTAAATT
2830872 TCAAATTCGCAACTAAATT
1 TCAAATTCGCAACTAAATT
2830891 TCAAATTCGCAAC
1 TCAAATTCGCAAC
2830904 GCGAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTAAATT
Found at i:2831839 original size:24 final size:24
Alignment explanation
Indices: 2831821--2831867 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2831811 AGTCAGTATT
2831821 CGAAATTTGATCTTGGTCAATACA
1 CGAAATTTGATCTTGGTCAATACA
* *
2831845 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
2831868 TCGGATTTTG
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:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACA
Found at i:2831872 original size:24 final size:24
Alignment explanation
Indices: 2831826--2831879 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2831816 GTATTCGAAA
2831826 TTTGATCTTGGTCAATACACGGAC
1 TTTGATCTTGGTCAATACACGGAC
* *
2831850 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACACGGAC
2831874 TTTGAT
1 TTTGAT
2831880 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACACGGAC
Found at i:2834520 original size:20 final size:20
Alignment explanation
Indices: 2834490--2834551 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
2834480 CGCGAAATAA
*
2834490 GCGTTGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
* *
2834510 GTGTAGCGAATTTGACTTTC
1 GCGTAGCGAATTTGACTATC
*
2834530 GCGTTGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
2834550 GC
1 GC
2834552 AACGCTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GCGTAGCGAATTTGACTATC
Found at i:2834680 original size:25 final size:25
Alignment explanation
Indices: 2834642--2834691 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2834632 AAATCAATTA
*
2834642 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2834667 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2834692 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:2835073 original size:24 final size:25
Alignment explanation
Indices: 2835046--2835097 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
2835036 TTTCAAATTC
*
2835046 ATTTTATATGT-AATTGGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
* *
2835070 A-TTTAAATTTCAATTTGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
2835094 ATTT
1 ATTT
2835098 CAATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTTAAATGTCAATTGGAGTTTGA
Found at i:2835086 original size:18 final size:18
Alignment explanation
Indices: 2835065--2835101 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2835055 GTAATTGGAG
2835065 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2835083 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2835101 T
1 T
2835102 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2835108 original size:24 final size:24
Alignment explanation
Indices: 2835057--2835109 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2835047 TTTTATATGT
* * *
2835057 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2835081 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
2835105 AATTT
1 AATTT
2835110 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2835490 original size:39 final size:39
Alignment explanation
Indices: 2835403--2835491 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
2835393 TCCGATGCTC
* *
2835403 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAATAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
2835442 ATCAAAATCTAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
2835481 ATCAAAATCTA
1 ATCAAAATCTA
2835492 CAACTTGGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:2837243 original size:21 final size:21
Alignment explanation
Indices: 2837204--2837301 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
2837194 ATGAATCAGG
* *
2837204 CTCTTGAACAATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
2837225 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
2837246 TTCTTCG-ATGATGATAGGGGC
1 CTCTT-GAACGATGAGAGGGGC
* *
2837267 CTCTTGAACGA-AATGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
*
2837288 CTCTTGAATGATGA
1 CTCTTGAACGATGA
2837302 TAGGTGCATC
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:2837299 original size:42 final size:42
Alignment explanation
Indices: 2837204--2837305 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
2837194 ATGAATCAGG
** * *** *
2837204 CTCTTGAACAATGACAGGGGCCTCTTGAACGGTGGGAGGGGC
1 CTCTTGAATGATGATAGGGGCCTCTTGAACGAAAGGAGGCGC
* *
2837246 TTCTTCG-ATGATGATAGGGGCCTCTTGAACGAAATGAGGCGC
1 CTCTT-GAATGATGATAGGGGCCTCTTGAACGAAAGGAGGCGC
2837288 CTCTTGAATGATGATAGG
1 CTCTTGAATGATGATAGG
2837306 TGCATCGGGT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGATGATAGGGGCCTCTTGAACGAAAGGAGGCGC
Found at i:2839219 original size:69 final size:69
Alignment explanation
Indices: 2839108--2839247 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
2839098 AATGCATCAG
2839108 ATAACATTCCAGAAGTAAGCACTTATATAAACATTTAAAAGGACAACATATAGGTTTAGTGCAGG
1 ATAACATTCCAGAAGTAAGCACTTATATAAACATTTAAAAGGACAACATATAGGTTTAGTGCAGG
2839173 TTCA
66 TTCA
2839177 ATAACATTCCAGAAGTAAGCACTTATATAAACATTTAAAAGGACAACATATAGGTTTAGTGCAGG
1 ATAACATTCCAGAAGTAAGCACTTATATAAACATTTAAAAGGACAACATATAGGTTTAGTGCAGG
2839242 TTCA
66 TTCA
2839246 AT
1 AT
2839248 GACAACATAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (69 bp):
ATAACATTCCAGAAGTAAGCACTTATATAAACATTTAAAAGGACAACATATAGGTTTAGTGCAGG
TTCA
Found at i:2839701 original size:22 final size:22
Alignment explanation
Indices: 2839672--2839744 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
2839662 GATGGAGATA
*
2839672 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAGATGGG
* *
2839694 AACGGATTTCATCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
2839716 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
2839738 GACGGAT
1 GACGGAT
2839745 GTCGCCGTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.23, C:0.12, G:0.41, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:2839897 original size:20 final size:20
Alignment explanation
Indices: 2839872--2839932 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
2839862 GCGTAAAAAC
2839872 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
2839892 ATTTGAC-TTCTGTGTTGTGA
1 ATTTGACTTTC-GCGTTGCGA
2839912 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2839932 A
1 A
2839933 ATTGGAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:2841092 original size:24 final size:25
Alignment explanation
Indices: 2841035--2841109 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
2841025 TTTAATATTT
* *
2841035 TTTATT-CTTTTTAAAATTTTATGAA
1 TTTATTCCTTCTTAAATTTTTAT-AA
2841060 TTTATTCCTTC-TAAATTTTTATAA
1 TTTATTCCTTCTTAAATTTTTATAA
2841084 GTTTA-TCCTTCTTAAATTTTTATAA
1 -TTTATTCCTTCTTAAATTTTTATAA
2841109 T
1 T
2841110 AAATTCGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 9 0.20
25 33 0.73
26 3 0.07
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTATTCCTTCTTAAATTTTTATAA
Found at i:2851163 original size:28 final size:29
Alignment explanation
Indices: 2851117--2851173 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2851107 CCTTTTTCAC
* *
2851117 TTAAAAAAATTAAAGTTCAATGA-GTAAA
1 TTAAAAAAATCAAACTTCAATGACGTAAA
*
2851145 TTAAAAAAATCAAACTTCAGTGACGTAAA
1 TTAAAAAAATCAAACTTCAATGACGTAAA
2851174 AACTAGCGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (29 bp):
TTAAAAAAATCAAACTTCAATGACGTAAA
Found at i:2856425 original size:4 final size:4
Alignment explanation
Indices: 2856416--2856441 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2856406 AATTTATGAT
2856416 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2856442 ATACCGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2858024 original size:14 final size:14
Alignment explanation
Indices: 2858005--2858043 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2857995 CTGTCTATAA
2858005 GCAGAGATTT-TTAC
1 GCAGAGATTTATT-C
*
2858019 GCAGAGATTTATTT
1 GCAGAGATTTATTC
2858033 GCAGAGATTTA
1 GCAGAGATTTA
2858044 CTAACCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (14 bp):
GCAGAGATTTATTC
Found at i:2858720 original size:20 final size:20
Alignment explanation
Indices: 2858683--2858720 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2858673 AATTTCAAAT
*
2858683 ATAATAACTTAGATTTTTTA
1 ATAATAACTTAGAATTTTTA
*
2858703 ATAATAACTTTGAATTTT
1 ATAATAACTTAGAATTTT
2858721 AACTCGTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
ATAATAACTTAGAATTTTTA
Found at i:2860921 original size:20 final size:21
Alignment explanation
Indices: 2860882--2860921 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2860872 AAAAAATTAT
* *
2860882 TTAAAATATTATTATTTTTAC
1 TTAAAATATCAATATTTTTAC
2860903 TTAAAATATCAAT-TTTTTA
1 TTAAAATATCAATATTTTTA
2860922 ATATTTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATATCAATATTTTTAC
Found at i:2860972 original size:11 final size:11
Alignment explanation
Indices: 2860943--2860975 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2860933 AAAAGTGTCC
2860943 AATAATAATAA
1 AATAATAATAA
2860954 AAT-A-AATAA
1 AATAATAATAA
2860963 AATAATAATAA
1 AATAATAATAA
2860974 AA
1 AA
2860976 CTGGTAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.40
10 2 0.10
11 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:2868069 original size:130 final size:130
Alignment explanation
Indices: 2867928--2868175 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
2867918 TATTTATATA
* *
2867928 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTATTCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
2867993 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
2868058 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
2868123 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
2868176 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:2868206 original size:130 final size:129
Alignment explanation
Indices: 2867942--2868206 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
2867932 ATTTGGTCCT
* * *
2867942 AAATTAAATAAAATTTAATAAATTATTCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
2868007 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
2868072 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
2868137 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
2868201 -A
128 CA
2868202 AAATT
1 AAATT
2868207 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:2868538 original size:28 final size:27
Alignment explanation
Indices: 2868507--2868569 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
2868497 AGTTGATACA
*
2868507 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
2868535 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
2868563 ATATTTT
1 ATATTTT
2868570 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:2868670 original size:16 final size:18
Alignment explanation
Indices: 2868649--2868682 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2868639 ATTTCTTATT
2868649 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2868665 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2868683 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2868829 original size:21 final size:21
Alignment explanation
Indices: 2868805--2868847 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2868795 TATTACCTTA
2868805 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2868826 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2868847 A
1 A
2868848 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:2868865 original size:35 final size:35
Alignment explanation
Indices: 2868816--2868901 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
2868806 ATTGAAGTAT
** * *
2868816 TTTAGAATTTAATTGAAGTA-TTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTGA-AAATTAGGG
* *
2868851 TTTAGAATAAAATTGAATTACTTTGAAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTGAAAATTAGGG
*
2868886 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
2868902 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 39 0.91
36 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTGAAAATTAGGG
Found at i:2885997 original size:27 final size:27
Alignment explanation
Indices: 2885976--2886028 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2885966 TAATATTGGA
*
2885976 ACCTTCATAAAAGAACAGAATAAGCAG
1 ACCTTCATAAAAAAACAGAATAAGCAG
2886003 ACCTTCATAAAAAAACAGAATAAGCA
1 ACCTTCATAAAAAAACAGAATAAGCA
2886029 ATGTTGAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (27 bp):
ACCTTCATAAAAAAACAGAATAAGCAG
Found at i:2894312 original size:12 final size:12
Alignment explanation
Indices: 2894280--2894319 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2894270 CAAAAAAATA
2894280 TTAAAA-TTA-T
1 TTAAAATTTATT
*
2894290 TT-AAATCTATT
1 TTAAAATTTATT
2894301 TTAAAATTTATT
1 TTAAAATTTATT
2894313 TTAAAAT
1 TTAAAAT
2894320 ATAGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:2894352 original size:26 final size:22
Alignment explanation
Indices: 2894306--2894362 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
2894296 CTATTTTAAA
2894306 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
2894328 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
2894350 ATTTATTTTAAAA
1 ATTTATTTTAAAA
2894363 AATTTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATAGATTG
Found at i:2894421 original size:31 final size:31
Alignment explanation
Indices: 2894386--2894445 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2894376 AGTTGTATGG
* **
2894386 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATATCAGTATTACAAAACTAAA
*
2894417 ATTATTTAAATATGAGTATTACAAAACTA
1 ATTATTTAAATATCAGTATTACAAAACTA
2894446 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTACAAAACTAAA
Found at i:2894510 original size:127 final size:124
Alignment explanation
Indices: 2894328--2894577 Score: 383
Period size: 127 Copynumber: 2.0 Consensus size: 124
2894318 ATATAGATTG
* ** *
2894328 ATTTATTTTAAAATATGAATTGATTTATTTTAAAAAATTTATTATTGTAGTTGTATGGATTATTT
1 ATTTATTTTAAAATATGAATTAATTTATTTTAAAAAAAATATTATTGTAATTGTATGGATTATTT
*
2894393 AAATTTCAGTATTGTAAAACTAAAATTATTTAAATATGAGTATTACAAAACTATTTTAAA
66 AAATTTCAGTATTGTAAAACTAAAATTATTTAAATAT-AATATTACAAAACTATTTTAAA
*
2894453 ATTTATTTTAAAATATGGATTAATTTATTTTTTAAAAAAAATATTATTGTAATTGTATGGATTAT
1 ATTTATTTTAAAATATGAATTAATTTA--TTTTAAAAAAAATATTATTGTAATTGTATGGATTAT
* * * *
2894518 TTAAATTTCAGTATTGTAAAATTAAAATTATTTAAATCTAATATTGCAAAACTCTTTTAA
64 TTAAATTTCAGTATTGTAAAACTAAAATTATTTAAATATAATATTACAAAACTATTTTAA
2894578 GTTAAAAAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 25 0.22
126 18 0.16
127 70 0.62
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (124 bp):
ATTTATTTTAAAATATGAATTAATTTATTTTAAAAAAAATATTATTGTAATTGTATGGATTATTT
AAATTTCAGTATTGTAAAACTAAAATTATTTAAATATAATATTACAAAACTATTTTAAA
Found at i:2894725 original size:223 final size:225
Alignment explanation
Indices: 2894453--2894858 Score: 611
Period size: 224 Copynumber: 1.8 Consensus size: 225
2894443 CTATTTTAAA
* *
2894453 ATTTATTTTAAAATATGGATTAATTTATTTTTTAAAAAAAATATTATTGTAATTGTATGGATTAT
1 ATTTATTTTAAAATATAGATTAATTTA-TTTTTAAAAAAAATATTATTGTAATTGTATAGATTAT
* * * * *
2894518 TTAAATTTCAGTAT-TGTAAAATTAAAATTATTTAAATCT-AATATTGCAAAACTCTTTTAAGTT
65 TTAAATTTCAGTATCT-TAAAACTAAAATGATTTAAATATCAATATTACAAAACTCGTTTAAGTT
*
2894581 AAAAAAATCAGTTTATTTATATTTTAGTTTATTTTAACAGTCTGCAGACGTTAATTTAATAAGGT
129 AAAAAAATCAGTTTATTTATATTTCAGTTTATTTTAACAGTCTGCAGACGTTAATTTAATAAGGT
2894646 TATTTATTAAATAATTTATTCAGTATGGATTG
194 TATTTATTAAATAATTTATTCAGTATGGATTG
* *** * *
2894678 ATTTATTTTAAAATATAGATTGATTTA-TTTTAAAAATTTTATTATTGTAGTTGTATATATTATT
1 ATTTATTTTAAAATATAGATTAATTTATTTTTAAAAAAAATATTATTGTAATTGTATAGATTATT
* *
2894742 TAAATTTCAGTATCTTAAAACTAAAATGATTTAAATATCAGTATTACAAAACTCGTTTAAGTTTA
66 TAAATTTCAGTATCTTAAAACTAAAATGATTTAAATATCAATATTACAAAACTCGTTTAAGTTAA
**
2894807 AAAAATCAGTTTATTTATATTTCAGTTTATTTTTGCAGTCTGCAGACGTTAA
131 AAAAATCAGTTTATTTATATTTCAGTTTATTTTAACAGTCTGCAGACGTTAA
2894859 AAAAACAATA
Statistics
Matches: 161, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
223 64 0.40
224 72 0.45
225 25 0.16
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.47
Consensus pattern (225 bp):
ATTTATTTTAAAATATAGATTAATTTATTTTTAAAAAAAATATTATTGTAATTGTATAGATTATT
TAAATTTCAGTATCTTAAAACTAAAATGATTTAAATATCAATATTACAAAACTCGTTTAAGTTAA
AAAAATCAGTTTATTTATATTTCAGTTTATTTTAACAGTCTGCAGACGTTAATTTAATAAGGTTA
TTTATTAAATAATTTATTCAGTATGGATTG
Found at i:2921403 original size:19 final size:20
Alignment explanation
Indices: 2921379--2921417 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2921369 ATTTCCCTTA
2921379 CTTAACCTTCCTTTC-TTTC
1 CTTAACCTTCCTTTCATTTC
*
2921398 CTTAACTTTCCTTTCATTTC
1 CTTAACCTTCCTTTCATTTC
2921418 TTTTCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.33, G:0.00, T:0.54
Consensus pattern (20 bp):
CTTAACCTTCCTTTCATTTC
Found at i:2925209 original size:79 final size:79
Alignment explanation
Indices: 2925041--2925214 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 79
2925031 CTACCTAATT
* * *
2925041 TTTTATTAAAAA-A-T-AATATTTTAAGTAGCAGTCAATATTAACATTTTCGGTATAAAAAATAA
1 TTTTATTAAAAATATTAAATATTTTAAGTAGAAGCCAATATTAACATTTTCAGTATAAAAAATAA
* *
2925103 TATTTTAGATAATA
66 TATTTTAAATAACA
* **** *
2925117 CTTTACCGGAAATATTAAATATTTTAAGTAGAAGCCAATATTAACATTTTTTAGTAT-AAAAATA
1 TTTTATTAAAAATATTAAATATTTTAAGTAGAAGCCAATATTAACA-TTTTCAGTATAAAAAATA
2925181 ATATTTTAAATAACA
65 ATATTTTAAATAACA
2925196 TTTTATTAAAAATATTAAA
1 TTTTATTAAAAATATTAAA
2925215 AAGATATTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
76 7 0.09
77 1 0.01
78 1 0.01
79 61 0.78
80 8 0.10
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (79 bp):
TTTTATTAAAAATATTAAATATTTTAAGTAGAAGCCAATATTAACATTTTCAGTATAAAAAATAA
TATTTTAAATAACA
Found at i:2926010 original size:60 final size:61
Alignment explanation
Indices: 2925917--2926043 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 61
2925907 TATATACATG
* * *
2925917 TAGTTT-GGGATGAAATTGAAATGTTTAAAAAGTTTGAGGACTAGTCTAGAATGA-AGGTCA
1 TAGTTTAGGGATGAAACTAAAATGTTTAAAAAGTTTGAGGACTAATCTAGAATGATA-GTCA
* * * *
2925977 TAGTTTAGGGATGGAACTAAAATG-TTCAAAAGTTTGAGGATTAATTTAGAATGATAGTCA
1 TAGTTTAGGGATGAAACTAAAATGTTTAAAAAGTTTGAGGACTAATCTAGAATGATAGTCA
2926037 TAGTTTA
1 TAGTTTA
2926044 AAGATTAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 43 0.74
61 15 0.26
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (61 bp):
TAGTTTAGGGATGAAACTAAAATGTTTAAAAAGTTTGAGGACTAATCTAGAATGATAGTCA
Found at i:2926914 original size:22 final size:24
Alignment explanation
Indices: 2926879--2926962 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 24
2926869 CTGTATATAT
2926879 ATATATATATATAATTGCATGATC
1 ATATATATATATAATTGCATGATC
****
2926903 ATAT-TATA-ATAATATG-AACCCC
1 ATATATATATATAAT-TGCATGATC
*
2926925 TTTATATATATATAATTGCATGATC
1 -ATATATATATATAATTGCATGATC
2926950 ATAT-TATA-ATAAT
1 ATATATATATATAAT
2926963 ATGAACCCCT
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
22 12 0.27
23 13 0.29
24 13 0.29
25 7 0.16
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (24 bp):
ATATATATATATAATTGCATGATC
Found at i:2926931 original size:47 final size:47
Alignment explanation
Indices: 2926880--2926976 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
2926870 TGTATATATA
2926880 TATATATATATAATTGCATGATCATATTATAATAATATGAACCCCTT
1 TATATATATATAATTGCATGATCATATTATAATAATATGAACCCCTT
2926927 TATATATATATAATTGCATGATCATATTATAATAATATGAACCCCTT
1 TATATATATATAATTGCATGATCATATTATAATAATATGAACCCCTT
2926974 TAT
1 TAT
2926977 TCATATCTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (47 bp):
TATATATATATAATTGCATGATCATATTATAATAATATGAACCCCTT
Found at i:2929014 original size:18 final size:19
Alignment explanation
Indices: 2928991--2929033 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2928981 CAATAATCCT
2928991 ATTCCCA-GGTAATCTTAC
1 ATTCCCACGGTAATCTTAC
*
2929009 ATTCCCACTGTTAATCTTAC
1 ATTCCCAC-GGTAATCTTAC
2929029 ATTCC
1 ATTCC
2929034 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCCACGGTAATCTTAC
Found at i:2929361 original size:19 final size:19
Alignment explanation
Indices: 2929337--2929373 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2929327 ATGACCAACA
*
2929337 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2929356 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2929374 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2929422 original size:20 final size:20
Alignment explanation
Indices: 2929399--2929522 Score: 101
Period size: 20 Copynumber: 6.2 Consensus size: 20
2929389 GTTTCCAAAT
*
2929399 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
2929419 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
2929439 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
2929459 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
2929480 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
2929500 TCACAATGCGA-TCTGACTA
1 TCGCAACGCGATTATGACTA
2929519 TCGC
1 TCGC
2929523 GTTGCGATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
19 13 0.16
20 52 0.63
21 16 0.19
22 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:2929443 original size:40 final size:42
Alignment explanation
Indices: 2929399--2929510 Score: 149
Period size: 40 Copynumber: 2.7 Consensus size: 42
2929389 GTTTCCAAAT
**
2929399 TCGCAACGCGATTTTGACTATCGCAATGCGAAT-ATGTA-AA
1 TCGCAACGCGATTTTGACTATCGCAATGCGAATAATACATAA
* * *
2929439 TCGCAATGCGATTCTGACTATCGCAACGCG-ATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAATGCGAATAATACATAA
*
2929480 TCGCAACGCGATTTTGACTATCACAATGCGA
1 TCGCAACGCGATTTTGACTATCGCAATGCGA
2929511 TCTGACTATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 30 0.50
41 28 0.47
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
TCGCAACGCGATTTTGACTATCGCAATGCGAATAATACATAA
Found at i:2929491 original size:41 final size:42
Alignment explanation
Indices: 2929399--2929511 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 42
2929389 GTTTCCAAAT
**
2929399 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTTTGACTATCGCAATGCGATAATACATAAA
* * *
2929439 TCGCAATGCGATTCTGACTATCGCAACGCGATAATACAT-AA
1 TCGCAACGCGATTTTGACTATCGCAATGCGATAATACATAAA
*
2929480 TCGCAACGCGATTTTGACTATCACAATGCGAT
1 TCGCAACGCGATTTTGACTATCGCAATGCGAT
2929512 CTGACTATCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 27 0.44
41 30 0.48
42 5 0.08
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
TCGCAACGCGATTTTGACTATCGCAATGCGATAATACATAAA
Found at i:2929714 original size:22 final size:23
Alignment explanation
Indices: 2929689--2929746 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
2929679 TCACTCTCTA
*
2929689 CGACGACATCCGTCCCCATCT-C
1 CGACGAAATCCGTCCCCATCTCC
*
2929711 CGACGAAATCCATCCCCATCTCC
1 CGACGAAATCCGTCCCCATCTCC
2929734 CG-CGAAATCCGTC
1 CGACGAAATCCGTC
2929747 TATCTCCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.22, C:0.47, G:0.14, T:0.17
Consensus pattern (23 bp):
CGACGAAATCCGTCCCCATCTCC
Done.