Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 16 of 17
Found at i:2347245 original size:19 final size:21
Alignment explanation
Indices: 2347218--2347259 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
2347208 TTTTAAATGT
2347218 AAATAATTA-AATT-ATATAA
1 AAATAATTACAATTAATATAA
* *
2347237 AAATTATTACACTTAATATAA
1 AAATAATTACAATTAATATAA
2347258 AA
1 AA
2347260 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAATTACAATTAATATAA
Found at i:2348764 original size:4 final size:4
Alignment explanation
Indices: 2348757--2348801 Score: 81
Period size: 4 Copynumber: 11.0 Consensus size: 4
2348747 CATTTGAAAG
2348757 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2348802 TATACATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:2349106 original size:45 final size:46
Alignment explanation
Indices: 2349055--2349147 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 46
2349045 TTGAAACCAC
* *
2349055 TCTATCATATTATTTTTGTG-TTTTTTTTAACTGTCTATCATAATT
1 TCTATCATATTATTTTTGTGTTTTTTTTTAACTATCTATCACAATT
2349100 TCTATCATATTATTTTTGTGTTTTTTTTTTAACTATCTATCACAATT
1 TCTATCATATTATTTTTGTG-TTTTTTTTTAACTATCTATCACAATT
2349147 T
1 T
2349148 TTATATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 20 0.45
47 24 0.55
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (46 bp):
TCTATCATATTATTTTTGTGTTTTTTTTTAACTATCTATCACAATT
Found at i:2351427 original size:33 final size:32
Alignment explanation
Indices: 2351385--2351453 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
2351375 AAAAATAAAC
* *
2351385 ATAACATAAATATATAAATATATTAAAA-TTTAT
1 ATAACATAAAT-TATAAACAT-CTAAAAGTTTAT
* *
2351418 ATAATATAAATTATTAACATCTAAAAGTTTAT
1 ATAACATAAATTATAAACATCTAAAAGTTTAT
2351450 ATAA
1 ATAA
2351454 ATTTATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 5 0.16
32 16 0.52
33 10 0.32
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAACATAAATTATAAACATCTAAAAGTTTAT
Found at i:2352333 original size:14 final size:13
Alignment explanation
Indices: 2352294--2352347 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
2352284 AATAAAATAT
2352294 TTAAT-TTT-TAA
1 TTAATATTTATAA
2352305 TTAATATTTATAA
1 TTAATATTTATAA
2352318 TTAA-ATTTAAATAA
1 TTAATATTT--ATAA
*
2352332 TTAATAATTAATAA
1 TTAAT-ATTTATAA
2352346 TT
1 TT
2352348 TTAGTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 5 0.14
12 7 0.19
13 7 0.19
14 14 0.39
16 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATATTTATAA
Found at i:2352339 original size:7 final size:7
Alignment explanation
Indices: 2352302--2352347 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2352292 ATTTAATTTT
2352302 TAATTAA
1 TAATTAA
*
2352309 T-ATTTA
1 TAATTAA
2352315 TAATTAA
1 TAATTAA
*
2352322 -ATTTAAA
1 TAATT-AA
2352329 TAATTAA
1 TAATTAA
2352336 TAATTAA
1 TAATTAA
2352343 TAATT
1 TAATT
2352348 TTAGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
6 8 0.25
7 21 0.66
8 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TAATTAA
Found at i:2353928 original size:2 final size:2
Alignment explanation
Indices: 2353921--2353952 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2353911 AACGAGTGAT
*
2353921 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2353953 AAAGTTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2355579 original size:3 final size:3
Alignment explanation
Indices: 2355571--2355622 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2355561 GGCAAAAGTC
2355571 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2355619 ATA A
1 ATA A
2355623 AGGTGAATTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2358288 original size:21 final size:21
Alignment explanation
Indices: 2358264--2358320 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2358254 TTACCAGTGA
*
2358264 TTCTCCCAGGTTTAACGTTGG
1 TTCTCCCAGGTTTAACATTGG
*
2358285 TTCTCCCAGGTATAACATTGG
1 TTCTCCCAGGTTTAACATTGG
2358306 TTCTCCCAGGTTTAA
1 TTCTCCCAGGTTTAA
2358321 TGCTAGCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (21 bp):
TTCTCCCAGGTTTAACATTGG
Found at i:2358788 original size:2 final size:2
Alignment explanation
Indices: 2358781--2358824 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2358771 AATAAGTGAT
2358781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2358823 TA
1 TA
2358825 CTGTACCACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2362117 original size:2 final size:2
Alignment explanation
Indices: 2362110--2362143 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2362100 TGATACTCTT
2362110 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
2362144 AAGAAAATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2363384 original size:18 final size:17
Alignment explanation
Indices: 2363361--2363394 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2363351 TCAAAAAAAA
2363361 TTAAAATTTAAGTTTAAG
1 TTAAAATTT-AGTTTAAG
2363379 TTAAAATTTAGTTTAA
1 TTAAAATTTAGTTTAA
2363395 ATTTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (17 bp):
TTAAAATTTAGTTTAAG
Found at i:2363470 original size:22 final size:22
Alignment explanation
Indices: 2363426--2363468 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2363416 AAATTATAAA
2363426 ATATAATTTTTAATTAATATTT
1 ATATAATTTTTAATTAATATTT
2363448 ATAT-ATTTTATAATTAA-ATTT
1 ATATAATTTT-TAATTAATATTT
2363469 TAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATAATTTTTAATTAATATTT
Found at i:2364640 original size:3 final size:3
Alignment explanation
Indices: 2364634--2364675 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
2364624 CTTTTTTTTC
2364634 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA
2364676 GTTTATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2373031 original size:28 final size:27
Alignment explanation
Indices: 2372999--2373051 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2372989 ACCCTTTTAA
*
2372999 TTTATTAAAAATGATGATTCTTTTTTTG
1 TTTATAAAAAATGATGATT-TTTTTTTG
*
2373027 TTTATAAAAAATGGTGATTTTTTTT
1 TTTATAAAAAATGATGATTTTTTTT
2373052 GTTCGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (27 bp):
TTTATAAAAAATGATGATTTTTTTTTG
Found at i:2377554 original size:24 final size:24
Alignment explanation
Indices: 2377522--2377567 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2377512 GAGATTCTTT
2377522 TTGTTTGTCAAAAATAGTGGCTTG
1 TTGTTTGTCAAAAATAGTGGCTTG
* *
2377546 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTCAAAAATAGTGGCT
2377568 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (24 bp):
TTGTTTGTCAAAAATAGTGGCTTG
Found at i:2382074 original size:42 final size:42
Alignment explanation
Indices: 2382013--2382131 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
2382003 TAGCCCTCAA
* *
2382013 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2382055 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACATG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
2382097 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2382132 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2387697 original size:22 final size:22
Alignment explanation
Indices: 2387664--2387710 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
2387654 TTTCAAATTA
2387664 AATATTAAT-AAATAAATAATAT
1 AATATTAATAAAATAAA-AATAT
2387686 AATA-TAATTAAAATAAAAATAT
1 AATATTAA-TAAAATAAAAATAT
2387708 AAT
1 AAT
2387711 TGCATCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.13
22 13 0.57
23 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATTAATAAAATAAAAATAT
Found at i:2392834 original size:17 final size:16
Alignment explanation
Indices: 2392797--2392849 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2392787 CGAATTAAAT
*
2392797 ATTAATAAATAA-ATA
1 ATTAAAAAATAATATA
*
2392812 AATAAACAAATAATATA
1 ATTAAA-AAATAATATA
*
2392829 ATTAAAATAAAAATATA
1 ATTAAAA-AATAATATA
2392846 ATTA
1 ATTA
2392850 CATCTCTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 20 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAAATAATATA
Found at i:2398926 original size:20 final size:20
Alignment explanation
Indices: 2398903--2398951 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2398893 ATATATAATT
*
2398903 TAAAATATAATTATAACATA
1 TAAAATATAATAATAACATA
2398923 TAAAA-ATATATAATAACATA
1 TAAAATATA-ATAATAACATA
*
2398943 -AATATATAA
1 TAAAATATAA
2398952 ATTTATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATATAATAATAACATA
Found at i:2399905 original size:21 final size:20
Alignment explanation
Indices: 2399881--2399953 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
2399871 ACAAAATAAA
2399881 TAAATAAATTATTAAAAATTT
1 TAAATAAATTA-TAAAAATTT
* * *
2399902 TAAATATAAATATAATATATAT
1 TAAATA-AATTATAA-AAATTT
* *
2399924 TAAATATATTATAATAATATT
1 TAAATAAATTATAAAAAT-TT
2399945 TAAATAAAT
1 TAAATAAAT
2399954 AATATGTTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.05
21 24 0.60
22 14 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAAATTATAAAAATTT
Found at i:2399928 original size:22 final size:21
Alignment explanation
Indices: 2399901--2399954 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2399891 ATTAAAAATT
2399901 TTAAATATAAATATAATATATA
1 TTAAATATAAATATAATA-ATA
*
2399923 TTAAATAT-ATTATAATAATA
1 TTAAATATAAATATAATAATA
*
2399943 TTTAA-ATAAATA
1 TTAAATATAAATA
2399955 ATATGTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 8 0.29
22 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATATAAATATAATAATA
Found at i:2401125 original size:2 final size:2
Alignment explanation
Indices: 2401118--2401149 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2401108 TTTCGTGCAC
*
2401118 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2401150 TATCATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2407906 original size:2 final size:2
Alignment explanation
Indices: 2407899--2407927 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2407889 ATCATATGTT
2407899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2407928 TAGTAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2408162 original size:28 final size:28
Alignment explanation
Indices: 2408089--2408165 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 28
2408079 TGTTCACTGT
*
2408089 TAAATTTAAATTTAATTAAATTAATTTA
1 TAAATTTAAATTTAAATAAATTAATTTA
*
2408117 TATAA-TTATATTTAAAATATAA-T-ATTTAA
1 TA-AATTTAAATTT-AAATA-AATTAATTT-A
2408146 TAAATTTAAATTTAAATAAA
1 TAAATTTAAATTTAAATAAA
2408166 AATACGACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.05
28 20 0.49
29 17 0.41
30 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATTTAAATTTAAATAAATTAATTTA
Found at i:2408169 original size:29 final size:28
Alignment explanation
Indices: 2408089--2408169 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
2408079 TGTTCACTGT
* *
2408089 TAAATTTAAATTT-AATTAAATTAATTTA
1 TAAATTTAAATTTAAATAAAAAT-ATTTA
* *
2408117 TATAA-TTATATTTAAA-ATATAATATTTAA
1 TA-AATTTAAATTTAAATA-AAAATATTT-A
2408146 TAAATTTAAATTTAAATAAAAATA
1 TAAATTTAAATTTAAATAAAAATA
2408170 CGACAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
28 15 0.37
29 25 0.61
30 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATTTAAATTTAAATAAAAATATTTA
Found at i:2408212 original size:22 final size:21
Alignment explanation
Indices: 2408172--2408212 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2408162 TAAAAATACG
* *
2408172 ACAATTTTTTTCTTCTAAATT
1 ACAATTTTTTTATTATAAATT
2408193 ACAATTTTTTTATATATAAA
1 ACAATTTTTTTAT-TATAAA
2408213 AAATTGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
ACAATTTTTTTATTATAAATT
Found at i:2408464 original size:22 final size:22
Alignment explanation
Indices: 2408429--2408470 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2408419 GGTTTCTCTG
** *
2408429 TTTTAATATTTAATTTATTACT
1 TTTTAATACATAATTAATTACT
2408451 TTTTAATACATAATTAATTA
1 TTTTAATACATAATTAATTA
2408471 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAATACATAATTAATTACT
Found at i:2408524 original size:3 final size:3
Alignment explanation
Indices: 2408516--2408541 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2408506 AATTTTATAC
2408516 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2408542 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2408701 original size:2 final size:2
Alignment explanation
Indices: 2408694--2408743 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2408684 TATCACCATC
2408694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2408736 AT AT AT AT
1 AT AT AT AT
2408744 CCAGACATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2411243 original size:2 final size:2
Alignment explanation
Indices: 2411236--2411270 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2411226 TATACGTAAG
2411236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2411271 ACAATATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2411490 original size:18 final size:16
Alignment explanation
Indices: 2411467--2411500 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2411457 ATGCTTAATA
2411467 AATTAAATAATATTATTT
1 AATTAAA-AA-ATTATTT
2411485 AATTAAAAAATTATTT
1 AATTAAAAAATTATTT
2411501 TTATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAAAATTATTT
Found at i:2411863 original size:21 final size:20
Alignment explanation
Indices: 2411837--2411892 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
2411827 TGGATTATTA
2411837 TTTAAATAATTTTTAAAAGTT
1 TTTAAATAATTTTTAAAA-TT
*
2411858 TTTAAATTTAA-ATTTAAAATT
1 TTTAAA--TAATTTTTAAAATT
*
2411879 TATAAATAATTTTT
1 TTTAAATAATTTTT
2411893 TTTATGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 13 0.45
22 7 0.24
23 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTAAATAATTTTTAAAATT
Found at i:2412268 original size:16 final size:16
Alignment explanation
Indices: 2412243--2412287 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2412233 AATTTTTACT
*
2412243 TAAATGTAATTTAATA
1 TAAATATAATTTAATA
*
2412259 TAAATATAATTTATTA
1 TAAATATAATTTAATA
2412275 -AATATATAATTTA
1 TAA-ATATAATTTA
2412288 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAAATATAATTTAATA
Found at i:2412288 original size:16 final size:16
Alignment explanation
Indices: 2412249--2412293 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2412239 TACTTAAATG
*
2412249 TAATTTAATATAA-ATA
1 TAATTTATTA-AATATA
2412265 TAATTTATTAAATATA
1 TAATTTATTAAATATA
2412281 TAATTTATTAAAT
1 TAATTTATTAAAT
2412294 TAAATGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTTATTAAATATA
Found at i:2412950 original size:2 final size:2
Alignment explanation
Indices: 2412943--2412973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2412933 TGGGATAATT
2412943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2412974 GTGCATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2419026 original size:114 final size:114
Alignment explanation
Indices: 2418821--2419048 Score: 377
Period size: 114 Copynumber: 2.0 Consensus size: 114
2418811 TATCAAGTGA
* *
2418821 GAAGTCAGTTTTTTATAAAAAGGGATCACATTATGATAAAGTACTGTAAAGATATAGCATATACC
1 GAAGCCAGTTTTTTATAAAAAGGGATCACATTATGATAAAGTACTGTAAAGATACAGCATATACC
* *
2418886 TCCCCAGATCCAAGGGATGAATTTATGCTCAGGAAACAGTTCCAAATCC
66 TCCCCAGATCCAAGGGATGAATTTATGCCCAGGAAACAGCTCCAAATCC
* * *
2418935 GAAGCCAGTTTTTTATAAAAGAGGG-TCACATTATGATCAAGTATTGTAAAGATACAGCGTATAC
1 GAAGCCAGTTTTTTATAAAA-AGGGATCACATTATGATAAAGTACTGTAAAGATACAGCATATAC
2418999 CTCCCCAGATCCAAGGGATGAATTTATGCCCAGGAAACAGCTCCAAATCC
65 CTCCCCAGATCCAAGGGATGAATTTATGCCCAGGAAACAGCTCCAAATCC
2419049 CAATAATTTG
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 102 0.96
115 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (114 bp):
GAAGCCAGTTTTTTATAAAAAGGGATCACATTATGATAAAGTACTGTAAAGATACAGCATATACC
TCCCCAGATCCAAGGGATGAATTTATGCCCAGGAAACAGCTCCAAATCC
Found at i:2419395 original size:24 final size:24
Alignment explanation
Indices: 2419349--2419395 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2419339 TTTAAATTTT
*
2419349 AATAAAATAAAAATATATTTAAAA
1 AATAAAATAAAAATATATATAAAA
*
2419373 AATAAATTAAAAATA-ATAATAAA
1 AATAAAATAAAAATATAT-ATAAA
2419396 TTAATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AATAAAATAAAAATATATATAAAA
Found at i:2420135 original size:4 final size:4
Alignment explanation
Indices: 2420128--2420233 Score: 59
Period size: 4 Copynumber: 24.0 Consensus size: 4
2420118 AATAACTAAA
**
2420128 AATT AATTT AAATT AATTT AATT AAAA AATT AATT AAATT AAATT AAATT
1 AATT AA-TT -AATT AA-TT AATT AATT AATT AATT -AATT -AATT -AATT
* * ** *
2420178 AATTT AGTT AATTT AATT TATT TTTT AATT AATTT AAAT AATT AATTT
1 AA-TT AATT AA-TT AATT AATT AATT AATT AA-TT AATT AATT AA-TT
2420226 AATT AATT
1 AATT AATT
2420234 TTTAGTTATT
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
4 43 0.52
5 37 0.45
6 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:2420143 original size:5 final size:5
Alignment explanation
Indices: 2420127--2420179 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
2420117 TAATAACTAA
* *
2420127 AAATT AATTT AAATT -AATT TAATT AAA-- AAATT -AATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
2420173 AAATT AA
1 AAATT AA
2420180 TTTAGTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.07
4 8 0.20
5 30 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:2420152 original size:9 final size:9
Alignment explanation
Indices: 2420128--2420234 Score: 87
Period size: 9 Copynumber: 12.0 Consensus size: 9
2420118 AATAACTAAA
2420128 AATTAATTT
1 AATTAATTT
2420137 AAATTAATTT
1 -AATTAATTT
**
2420147 AATTAA-AA
1 AATTAATTT
*
2420155 AATTAATTA
1 AATTAATTT
*
2420164 AATTAAATTA
1 AATT-AATTT
2420174 AATTAATTT
1 AATTAATTT
*
2420183 AGTTAATTT
1 AATTAATTT
*
2420192 AATTTATTT
1 AATTAATTT
*
2420201 -TTTAA-TT
1 AATTAATTT
*
2420208 AATTTAA-AT
1 AA-TTAATTT
2420217 AATTAATTT
1 AATTAATTT
2420226 AATTAATTT
1 AATTAATTT
2420235 TTAGTTATTA
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
7 2 0.03
8 13 0.16
9 47 0.59
10 18 0.22
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:2420348 original size:22 final size:22
Alignment explanation
Indices: 2420323--2420378 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2420313 ATATAAATTT
*
2420323 AAACTTAAATTCTTTAAACTAA
1 AAACTTAAATTATTTAAACTAA
* * *
2420345 AAACTTATATAAATTTAAATTAA
1 AAACTTAAAT-TATTTAAACTAA
2420368 AAAC-TAAATTA
1 AAACTTAAATTA
2420379 AAACAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.04
22 13 0.48
23 13 0.48
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
AAACTTAAATTATTTAAACTAA
Found at i:2420505 original size:21 final size:21
Alignment explanation
Indices: 2420479--2420519 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2420469 AATCTATTTA
*
2420479 ATCGATTTTGATATCGATTCG
1 ATCGATTTTAATATCGATTCG
2420500 ATCGATTTTAATATCGATTC
1 ATCGATTTTAATATCGATTC
2420520 AATTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (21 bp):
ATCGATTTTAATATCGATTCG
Found at i:2420529 original size:20 final size:21
Alignment explanation
Indices: 2420478--2420530 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2420468 TAATCTATTT
*
2420478 AATCGATTTTGATATCGATTC
1 AATCGATTTTAATATCGATTC
*
2420499 GATCGATTTTAATATCGATTC
1 AATCGATTTTAATATCGATTC
*
2420520 AAT-TATTTTAA
1 AATCGATTTTAA
2420531 CTTTAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (21 bp):
AATCGATTTTAATATCGATTC
Found at i:2420602 original size:26 final size:28
Alignment explanation
Indices: 2420547--2420615 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
2420537 ATTTAAAATC
*
2420547 AATTAATTTAATTAA-TTTTAATATTAA
1 AATTAATTAAATTAATTTTTAATATTAA
2420574 AATTAATTAAATTAATTTTTAAT-TT-A
1 AATTAATTAAATTAATTTTTAATATTAA
* *
2420600 AATAAATTAAACTAAT
1 AATTAATTAAATTAAT
2420616 CGAACCTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.39
27 16 0.42
28 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTAATTAAATTAATTTTTAATATTAA
Found at i:2420605 original size:21 final size:21
Alignment explanation
Indices: 2420549--2420609 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2420539 TTAAAATCAA
*
2420549 TTAATTTAATTAATTTTAATAT
1 TTAATTTAATTAA-ATTAATAT
* * *
2420571 TAAAATTAATTAAATTAATTT
1 TTAATTTAATTAAATTAATAT
*
2420592 TTAATTTAAATAAATTAA
1 TTAATTTAATTAAATTAA
2420610 ACTAATCGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATTTAATTAAATTAATAT
Found at i:2424491 original size:27 final size:26
Alignment explanation
Indices: 2424439--2424490 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2424429 TTGCTATCTG
2424439 CCTTTTTGTTTTCTGTTCATTAAAAA
1 CCTTTTTGTTTTCTGTTCATTAAAAA
2424465 CCTTTTTGTTTTCTGTTCATTAAAAA
1 CCTTTTTGTTTTCTGTTCATTAAAAA
2424491 AAAAGGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (26 bp):
CCTTTTTGTTTTCTGTTCATTAAAAA
Found at i:2426351 original size:19 final size:20
Alignment explanation
Indices: 2426316--2426354 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2426306 ATTAAATAAT
2426316 TTTAATATATATATTTTATA
1 TTTAATATATATATTTTATA
*
2426336 TTTAATA-ATTTATTTTATA
1 TTTAATATATATATTTTATA
2426355 ATTTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATATATATATTTTATA
Found at i:2426358 original size:20 final size:21
Alignment explanation
Indices: 2426311--2426358 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
2426301 AGTGGATTAA
2426311 ATAATTTTAATATATATATTTT
1 ATAA-TTTAATATATATATTTT
*
2426333 AT-ATTTAATA-ATTTATTTT
1 ATAATTTAATATATATATTTT
2426352 ATAATTT
1 ATAATTT
2426359 TTTAGAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.42
20 11 0.46
21 1 0.04
22 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAATTTAATATATATATTTT
Found at i:2426748 original size:22 final size:21
Alignment explanation
Indices: 2426707--2426765 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
2426697 CGAATTTTTT
2426707 ATTATTTAAA--TAATAATAA
1 ATTATTTAAATTTAATAATAA
*
2426726 ATTATTTAAATTTAATTATTAA
1 ATTATTTAAATTTAA-TAATAA
* *
2426748 AGTATGTAAATTTTAATA
1 ATTATTTAAA-TTTAATA
2426766 TGTTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 10 0.30
21 3 0.09
22 15 0.45
23 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTATTTAAATTTAATAATAA
Found at i:2428583 original size:16 final size:15
Alignment explanation
Indices: 2428564--2428610 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2428554 TAAACATGTA
*
2428564 ATATTTAATACATAAT
1 ATATTTAA-AAATAAT
2428580 ATATTTAAAAATAAT
1 ATATTTAAAAATAAT
* *
2428595 ATA-ATAAATATAAT
1 ATATTTAAAAATAAT
2428609 AT
1 AT
2428611 GATATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 11 0.39
15 9 0.32
16 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTTAAAAATAAT
Found at i:2429342 original size:6 final size:6
Alignment explanation
Indices: 2429321--2429364 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
2429311 TTTGGGTTTC
2429321 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
2429365 GGCCAATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:2429752 original size:2 final size:2
Alignment explanation
Indices: 2429745--2429776 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2429735 TATTAAAATA
*
2429745 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2429777 TTCGAGGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2434777 original size:22 final size:21
Alignment explanation
Indices: 2434742--2434783 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2434732 TACGAGAGAA
*
2434742 AAAAAATTATTTAAAAATAAT
1 AAAAAATAATTTAAAAATAAT
*
2434763 AAAAAATAATATTAAATATAA
1 AAAAAATAAT-TTAAAAATAA
2434784 ATATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATAATTTAAAAATAAT
Found at i:2434796 original size:23 final size:21
Alignment explanation
Indices: 2434770--2434825 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
2434760 AATAAAAAAT
2434770 AATATTAAATATAAATATATTAA
1 AATATTAAA-A-AAATATATTAA
*
2434793 AATATTTATAAAAAATTTATTAA
1 AATA-TTA-AAAAAATATATTAA
*
2434816 TATATTAAAA
1 AATATTAAAA
2434826 TTTATATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
23 17 0.59
24 4 0.14
25 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATTAAAAAAATATATTAA
Found at i:2434827 original size:18 final size:20
Alignment explanation
Indices: 2434804--2434840 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2434794 ATATTTATAA
2434804 AAAATTTAT-TA-ATATATT
1 AAAATTTATATACATATATT
2434822 AAAATTTATATACATATAT
1 AAAATTTATATACATATAT
2434841 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATTTATATACATATATT
Found at i:2435182 original size:16 final size:17
Alignment explanation
Indices: 2435163--2435225 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
2435153 TTTTTAGTAG
2435163 TTTTTAAAAATTAT-TA
1 TTTTTAAAAATTATATA
* *
2435179 TTTTTTAATAA-TATAAA
1 -TTTTTAAAAATTATATA
* *
2435196 ATTTTAAAAAGTATATA
1 TTTTTAAAAATTATATA
2435213 TTTATTAAAAATT
1 TTT-TTAAAAATT
2435226 TATTTAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
16 11 0.31
17 17 0.47
18 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTTAAAAATTATATA
Found at i:2435185 original size:17 final size:17
Alignment explanation
Indices: 2435163--2435225 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 17
2435153 TTTTTAGTAG
2435163 TTTTTAAAAATTATTAT
1 TTTTTAAAAATTATTAT
* * *
2435180 TTTTTAATAA-TATAAA
1 TTTTTAAAAATTATTAT
* *
2435196 ATTTTAAAAAGTATATAT
1 TTTTTAAAAATTAT-TAT
*
2435214 TTATTAAAAATT
1 TTTTTAAAAATT
2435226 TATTTAAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
16 12 0.35
17 12 0.35
18 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTTAAAAATTATTAT
Found at i:2435680 original size:13 final size:13
Alignment explanation
Indices: 2435657--2435690 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2435647 ATTATTTATA
*
2435657 AATAAAAATAAAT
1 AATAAATATAAAT
*
2435670 AGTAAATATAAAT
1 AATAAATATAAAT
2435683 AATAAATA
1 AATAAATA
2435691 ATATAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AATAAATATAAAT
Found at i:2436040 original size:26 final size:26
Alignment explanation
Indices: 2436008--2436079 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
2435998 AAATATATTA
2436008 AAAATAATTAAATTTTAATATAAAAT
1 AAAATAATTAAATTTTAATATAAAAT
2436034 AAAATAA-T-AATTAATTAATAT-AAAT
1 AAAATAATTAAATT--TTAATATAAAAT
* *
2436059 ATAAT-ATTAAATTTAAATATA
1 AAAATAATTAAATTTTAATATA
2436080 TTTAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
24 11 0.28
25 10 0.26
26 18 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAATAATTAAATTTTAATATAAAAT
Found at i:2436063 original size:11 final size:11
Alignment explanation
Indices: 2435973--2436070 Score: 58
Period size: 13 Copynumber: 8.5 Consensus size: 11
2435963 TTAATAATTT
*
2435973 TAAATGTAATA
1 TAAATATAATA
2435984 TAATTATATAATA
1 TAA--ATATAATA
2435997 TAAATAT-AT-
1 TAAATATAATA
*
2436006 TAAAAATAAT-
1 TAAATATAATA
*
2436016 TAAATTTTAATA
1 TAAA-TATAATA
*
2436028 TAAAATAAAATAA
1 T-AAATATAAT-A
*
2436041 TAATTAATTAATA
1 TAAAT-A-TAATA
2436054 TAAATATAATA
1 TAAATATAATA
2436065 TTAAAT
1 -TAAAT
2436071 TTAAATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 6 0.09
10 8 0.12
11 16 0.24
12 14 0.21
13 21 0.31
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2436086 original size:16 final size:18
Alignment explanation
Indices: 2436054--2436088 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2436044 TTAATTAATA
2436054 TAAATATAATATTAAATT
1 TAAATATAATATTAAATT
2436072 TAAATAT-AT-TTAAATT
1 TAAATATAATATTAAATT
2436088 T
1 T
2436089 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATATAATATTAAATT
Found at i:2436101 original size:9 final size:9
Alignment explanation
Indices: 2436073--2436130 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
2436063 TATTAAATTT
*
2436073 AAATATATTT
1 AAAT-TATTA
*
2436083 AAATTTTTA
1 AAATTATTA
2436092 AAATTATTA
1 AAATTATTA
2436101 AAATTA-TA
1 AAATTATTA
*
2436109 ATA-TATTA
1 AAATTATTA
2436117 AAA-TA-TA
1 AAATTATTA
2436124 AAATTAT
1 AAATTAT
2436131 AATATCAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
7 7 0.17
8 12 0.30
9 17 0.43
10 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATTATTA
Found at i:2436117 original size:16 final size:16
Alignment explanation
Indices: 2436062--2436124 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
2436052 TATAAATATA
*
2436062 ATATTAAATTTA-AAT
1 ATATTAAAATTATAAT
* * *
2436077 ATATTTAAATTTTTAAA
1 ATA-TTAAAATTATAAT
2436094 ATTATTAAAATTATAAT
1 A-TATTAAAATTATAAT
2436111 ATATTAAAA-TATAA
1 ATATTAAAATTATAA
2436125 AATTATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 8 0.20
16 16 0.40
17 14 0.35
18 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAAATTATAAT
Found at i:2436128 original size:23 final size:25
Alignment explanation
Indices: 2436089--2436135 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 25
2436079 ATTTAAATTT
2436089 TTAAAATTATTAAAATTATAATATA
1 TTAAAATTATTAAAATTATAATATA
2436114 TTAAAA-TA-TAAAATTATAATAT
1 TTAAAATTATTAAAATTATAATAT
2436136 CAATATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.64
24 2 0.09
25 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAATTATTAAAATTATAATATA
Found at i:2436508 original size:16 final size:16
Alignment explanation
Indices: 2436468--2436542 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
2436458 ATTTTGGAAA
* *
2436468 AATAATAATTTAGTTT
1 AATAAAAATTTAATTT
**
2436484 AATTCAAATTTAATTT
1 AATAAAAATTTAATTT
2436500 AATAAAAATTTTAATTTT
1 AATAAAAA-TTTAA-TTT
*
2436518 AATTTAAAA--TAATTT
1 AA-TAAAAATTTAATTT
2436533 AAATAAAAAT
1 -AATAAAAAT
2436543 ATTTAAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
15 8 0.17
16 23 0.50
17 5 0.11
18 5 0.11
19 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
AATAAAAATTTAATTT
Found at i:2436546 original size:14 final size:15
Alignment explanation
Indices: 2436523--2436564 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
2436513 ATTTTAATTT
2436523 AAAATAATTTAAATA
1 AAAATAATTTAAATA
*
2436538 AAAAT-ATTTAAATT
1 AAAATAATTTAAATA
*
2436552 TAAATAATTTAAA
1 AAAATAATTTAAA
2436565 ATTTTAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATAATTTAAATA
Found at i:2436570 original size:23 final size:24
Alignment explanation
Indices: 2436538--2436583 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2436528 AATTTAAATA
*
2436538 AAAATATTTAAATTTAAATAATTT
1 AAAATATTTAAATTAAAATAATTT
*
2436562 AAAAT-TTTAACTTAAAATAATT
1 AAAATATTTAAATTAAAATAATT
2436584 ATAATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATATTTAAATTAAAATAATTT
Found at i:2437681 original size:19 final size:18
Alignment explanation
Indices: 2437637--2437682 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2437627 TATAATTTGA
2437637 ATTAATTATTTTAAAACAT
1 ATTAA-TATTTTAAAACAT
2437656 A--AATATTTTAGAAACAT
1 ATTAATATTTTA-AAACAT
2437673 ATTAATATTT
1 ATTAATATTT
2437683 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.29
17 9 0.38
19 8 0.33
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTAATATTTTAAAACAT
Found at i:2437859 original size:18 final size:18
Alignment explanation
Indices: 2437825--2437867 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2437815 ATTTAAATTA
*
2437825 AATTTATAATTATTAAAT
1 AATTTATAAATATTAAAT
*
2437843 AATTTATAAAATATAAAAT
1 AATTTAT-AAATATTAAAT
2437862 -ATTTAT
1 AATTTAT
2437868 TTAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTATAAATATTAAAT
Found at i:2438142 original size:15 final size:16
Alignment explanation
Indices: 2438119--2438152 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2438109 ATTATAATTT
*
2438119 AAATTAAAATTTTA-A
1 AAATAAAAATTTTATA
2438134 AAATAAAAATTTTATA
1 AAATAAAAATTTTATA
2438150 AAA
1 AAA
2438153 AATGAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAAAAATTTTATA
Found at i:2440278 original size:2 final size:2
Alignment explanation
Indices: 2440271--2440304 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2440261 AAATTGTTAT
2440271 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
2440305 ATGGAAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2446942 original size:41 final size:43
Alignment explanation
Indices: 2446897--2446993 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 43
2446887 TTATTTTAAA
2446897 AATTTAATTTAAATTAAATTAATT-TT-TTTAA-AAAAATTATT
1 AATTTAATTTAAATTAAATT-ATTATTATTTAACAAAAATTATT
* *
2446938 AATTTAAATTAATTTAAATTATTATTAATTTAACAAAAATTATT
1 AATTTAATTTAAATTAAATTATTATT-ATTTAACAAAAATTATT
2446982 --TTT-ATTTAAATT
1 AATTTAATTTAAATT
2446994 TATTATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
40 3 0.06
41 27 0.56
42 3 0.06
43 5 0.10
44 10 0.21
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
AATTTAATTTAAATTAAATTATTATTATTTAACAAAAATTATT
Found at i:2446944 original size:26 final size:25
Alignment explanation
Indices: 2446909--2446970 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
2446899 TTTAATTTAA
* **
2446909 ATTAAATTAATTTTTTTAAAAAAATT
1 ATTAATTTAATTAATTT-AAAAAATT
**
2446935 ATTAATTTAAATTAATTTAAATTATT
1 ATTAATTT-AATTAATTTAAAAAATT
2446961 ATTAATTTAA
1 ATTAATTTAA
2446971 CAAAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.07
26 21 0.70
27 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAATTTAATTAATTTAAAAAATT
Found at i:2446976 original size:46 final size:46
Alignment explanation
Indices: 2446900--2446993 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 46
2446890 TTTTAAAAAT
***
2446900 TTAATTTAAATTAAATTAATTTTTTTAAAAA-AATTATTAATTTAAA
1 TTAATTTAAATTAAATTAATTTTAACAAAAATAATT-TTAATTTAAA
* * *
2446946 TTAATTTAAATTATTATTAA-TTTAACAAAAATTATTTTTATTTAAA
1 TTAATTTAAATTA-AATTAATTTTAACAAAAATAATTTTAATTTAAA
2446992 TT
1 TT
2446994 TATTATAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
46 32 0.80
47 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (46 bp):
TTAATTTAAATTAAATTAATTTTAACAAAAATAATTTTAATTTAAA
Found at i:2448089 original size:22 final size:20
Alignment explanation
Indices: 2448047--2448090 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2448037 TTTAATTAAA
*
2448047 AATATATAAAATAAAATTTT
1 AATATATAAAATAAAAATTT
*
2448067 AATATATTTAAATAATAAATTT
1 AATATA-TAAAATAA-AAATTT
2448089 AA
1 AA
2448091 ATCATTGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATATAAAATAAAAATTT
Found at i:2448664 original size:28 final size:29
Alignment explanation
Indices: 2448608--2448665 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
2448598 AATGATATAT
* *
2448608 ATTTTATTTATTTTATAATGAATTTATAA
1 ATTTTATTTATTATATAATGAATTAATAA
2448637 ATTTTATTT-TTATATAAT-AATCTAATAA
1 ATTTTATTTATTATATAATGAAT-TAATAA
2448665 A
1 A
2448666 ATAAATTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 14 0.54
29 9 0.35
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTTATTTATTATATAATGAATTAATAA
Found at i:2449840 original size:78 final size:77
Alignment explanation
Indices: 2449731--2449884 Score: 200
Period size: 77 Copynumber: 2.0 Consensus size: 77
2449721 ATCTTTATAA
* * * * *
2449731 AAATTTTATTGTTCATCTATTTATTAATTAAAGTTAAAAAGTTACGAAATATTAAAGTAAAATTT
1 AAATTTTATTATTCATCTATCTATTAATTAAACTT-AAAAGTTACAAAATATTAAAGTAAAACTT
2449796 TAATTGTCAAGTC
65 TAATTGTCAAGTC
* * * * *
2449809 AAATTTTATTATTTATTTATCTATTAGTTAAACTTAAAAGTTACAAAATTTTATAGTAAAACTTT
1 AAATTTTATTATTCATCTATCTATTAATTAAACTTAAAAGTTACAAAATATTAAAGTAAAACTTT
*
2449874 AATTGTTAAGT
66 AATTGTCAAGT
2449885 TATGTAACAC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
77 36 0.55
78 29 0.45
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (77 bp):
AAATTTTATTATTCATCTATCTATTAATTAAACTTAAAAGTTACAAAATATTAAAGTAAAACTTT
AATTGTCAAGTC
Found at i:2450543 original size:29 final size:32
Alignment explanation
Indices: 2450508--2450575 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
2450498 AACCTTTTTT
*
2450508 AAGTTATAG-ATG-AT-AAATATAATTTTTAA
1 AAGTTATAGTATGAATAAAATATAACTTTTAA
*
2450537 AAGTTAT-GTATGAATAAAATGTAACTTTTAA
1 AAGTTATAGTATGAATAAAATATAACTTTTAA
*
2450568 AAATTATA
1 AAGTTATA
2450576 AATAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 10 0.31
30 2 0.06
31 19 0.59
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (32 bp):
AAGTTATAGTATGAATAAAATATAACTTTTAA
Found at i:2452389 original size:17 final size:19
Alignment explanation
Indices: 2452347--2452389 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2452337 TTTATTTAAT
*
2452347 AAAATATTTATCAAATATA
1 AAAATTTTTATCAAATATA
*
2452366 AATATTTTTATCAAA-A-A
1 AAAATTTTTATCAAATATA
2452383 AAAATTT
1 AAAATTT
2452390 AAACACTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTTTATCAAATATA
Found at i:2453294 original size:12 final size:12
Alignment explanation
Indices: 2453277--2453305 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2453267 ATAAATAAAT
2453277 AGAAAAAAATAG
1 AGAAAAAAATAG
2453289 AGAAAAAAATAG
1 AGAAAAAAATAG
2453301 A-AAAA
1 AGAAAA
2453306 TAAAACCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AGAAAAAAATAG
Found at i:2460755 original size:3 final size:3
Alignment explanation
Indices: 2460747--2460776 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2460737 TTAATTATTT
2460747 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2460777 TATCATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2460997 original size:15 final size:15
Alignment explanation
Indices: 2460959--2460997 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2460949 TAAATGGATT
2460959 AATAATTATTTTTAAA
1 AATAATTA-TTTTAAA
*
2460975 AAT-TTTATTTTAAA
1 AATAATTATTTTAAA
2460989 AATAATTAT
1 AATAATTAT
2460998 ATATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.50
15 7 0.35
16 3 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATAATTATTTTAAA
Found at i:2467672 original size:47 final size:46
Alignment explanation
Indices: 2467618--2467708 Score: 173
Period size: 47 Copynumber: 2.0 Consensus size: 46
2467608 AAGACTATAT
2467618 ATCTCAAAGTTAATGCTTAGTTAACAAAGTAATGGGCTGAAGAATCA
1 ATCTCAAAGTTAATGCTTAGTTAACAAAGTAATGGG-TGAAGAATCA
2467665 ATCTCAAAGTTAATGCTTAGTTAACAAAGTAATGGGTGAAGAAT
1 ATCTCAAAGTTAATGCTTAGTTAACAAAGTAATGGGTGAAGAAT
2467709 TAATACATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 8 0.18
47 36 0.82
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (46 bp):
ATCTCAAAGTTAATGCTTAGTTAACAAAGTAATGGGTGAAGAATCA
Found at i:2467835 original size:25 final size:24
Alignment explanation
Indices: 2467794--2467844 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2467784 ATATAAAAAT
*
2467794 ATTTTTTTATAAAAATTTAATTTA
1 ATTTTTTTATAAAAATTAAATTTA
2467818 ATTTTATTTA-AAATAATTAAATTTA
1 ATTTT-TTTATAAA-AATTAAATTTA
2467843 AT
1 AT
2467845 ATAATTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTTTATAAAAATTAAATTTA
Found at i:2468311 original size:30 final size:29
Alignment explanation
Indices: 2468256--2468312 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
2468246 TTTTAAAAGA
*
2468256 TAAAATTATAAATATTATGATTTAAATTT
1 TAAAATTATAAATATTATAATTTAAATTT
*
2468285 TAAATTTATTAAATATTA-AATATTAAAT
1 TAAAATTA-TAAATATTATAAT-TTAAAT
2468313 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATTATAAATATTATAATTTAAATTT
Found at i:2468313 original size:7 final size:7
Alignment explanation
Indices: 2468264--2468314 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
2468254 GATAAAATTA
2468264 TAAATAT
1 TAAATAT
*
2468271 TATGAT-T
1 TA-AATAT
*
2468278 TAAATTT
1 TAAATAT
2468285 TAAATTTAT
1 TAAA--TAT
2468294 TAAATAT
1 TAAATAT
2468301 TAAATAT
1 TAAATAT
2468308 TAAATAT
1 TAAATAT
2468315 ATTTAAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
6 2 0.05
7 27 0.73
8 2 0.05
9 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (7 bp):
TAAATAT
Found at i:2468466 original size:19 final size:19
Alignment explanation
Indices: 2468434--2468472 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2468424 AAATTTGATT
2468434 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
2468453 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
2468472 T
1 T
2468473 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:2468608 original size:2 final size:2
Alignment explanation
Indices: 2468597--2468625 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2468587 TCAATTTGTG
2468597 TA TA TA -A 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
2468626 AATAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2469279 original size:19 final size:17
Alignment explanation
Indices: 2469232--2469279 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
2469222 AATGGGAAGC
2469232 TAAAAAAAATAAAAAATT
1 TAAAAAAAA-AAAAAATT
*
2469250 TAAATAAAAAACTAAAATT
1 TAAA-AAAAAA-AAAAATT
2469269 TAAAAAAAAAA
1 TAAAAAAAAAA
2469280 TAGAGGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAAAAAAAAATT
Found at i:2469358 original size:2 final size:2
Alignment explanation
Indices: 2469353--2469382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2469343 TATATAAAGA
2469353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2469383 GAAATCAATG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2469841 original size:23 final size:24
Alignment explanation
Indices: 2469810--2469857 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2469800 ATAGTTTTTA
*
2469810 TTTTATTTT-ATATTTTTAAAATT
1 TTTTATTTTAATATTATTAAAATT
* *
2469833 TTTTCTTTTAATATTATTAATATT
1 TTTTATTTTAATATTATTAAAATT
2469857 T
1 T
2469858 ATATGATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATTTTAATATTATTAAAATT
Found at i:2470659 original size:24 final size:23
Alignment explanation
Indices: 2470622--2470671 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2470612 ATAAAATTTT
*
2470622 TTAATTAAATTTAATTATAAATA
1 TTAATTAAAATTAATTATAAATA
* *
2470645 TTAATATAAAATTAATTTTTAATA
1 TTAAT-TAAAATTAATTATAAATA
2470669 TTA
1 TTA
2470672 TTTTAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATTAAAATTAATTATAAATA
Found at i:2470678 original size:24 final size:24
Alignment explanation
Indices: 2470622--2470678 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2470612 ATAAAATTTT
*
2470622 TTAA-TTAAATTTAATTATAAATA
1 TTAATTTAAAATTAATTATAAATA
* * *
2470645 TTAATATAAAATTAATTTTTAATA
1 TTAATTTAAAATTAATTATAAATA
*
2470669 TTATTTTAAA
1 TTAATTTAAA
2470679 TAGTAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTTAAAATTAATTATAAATA
Found at i:2470680 original size:12 final size:13
Alignment explanation
Indices: 2470626--2470680 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
2470616 AATTTTTTAA
2470626 TTAAAT-TTAATT
1 TTAAATATTAATT
*
2470638 ATAAATATTAA-T
1 TTAAATATTAATT
*
2470650 ATAAA-ATTAATT
1 TTAAATATTAATT
*
2470662 TTTAATATT-ATT
1 TTAAATATTAATT
2470674 TTAAATA
1 TTAAATA
2470681 GTAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 24 0.67
13 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAAATATTAATT
Found at i:2471435 original size:3 final size:3
Alignment explanation
Indices: 2471429--2471459 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2471419 AATGATGATG
*
2471429 ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2471460 AATTATGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2475599 original size:4 final size:4
Alignment explanation
Indices: 2475590--2475618 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2475580 TTAGCCTGGC
2475590 TCTT TCTT TCTT TCTT TCTT T-TT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
2475619 AACTAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:2476190 original size:18 final size:18
Alignment explanation
Indices: 2476153--2476196 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2476143 ATCATTTAGA
*
2476153 TATAAATATATTACAAAT
1 TATAAATATATTAAAAAT
2476171 TATTAAATAT-TTAAAAAT
1 TA-TAAATATATTAAAAAT
2476189 TATAAATA
1 TATAAATA
2476197 AAAATACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 11 0.46
19 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATATTAAAAAT
Found at i:2477605 original size:24 final size:25
Alignment explanation
Indices: 2477585--2477657 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 25
2477575 GTTATTAAGT
*
2477585 TAAAAAT-ATTAAATATAATT-ATA
1 TAAAAATAATAAAATATAATTAATA
*
2477608 TAAAAATAATAAAATATAATTAAAA
1 TAAAAATAATAAAATATAATTAATA
* *
2477633 TATAATATAAAATAAATAT-ATTAAT
1 TA-AAAATAATA-AAATATAATTAAT
2477658 TAGTATTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 7 0.17
24 12 0.29
25 4 0.10
26 12 0.29
27 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAATAATAAAATATAATTAATA
Found at i:2477633 original size:11 final size:11
Alignment explanation
Indices: 2477608--2477646 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2477598 TATAATTATA
2477608 TAAAA-ATAA-
1 TAAAATATAAT
2477617 TAAAATATAAT
1 TAAAATATAAT
2477628 TAAAATATAAT
1 TAAAATATAAT
2477639 ATAAAATA
1 -TAAAATA
2477647 AATATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 11 0.41
12 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:2477639 original size:21 final size:20
Alignment explanation
Indices: 2477608--2477647 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2477598 TATAATTATA
2477608 TAAAAATAATA-AAATATAAT
1 TAAAAATAATATAAA-ATAAT
2477628 TAAAATATAATATAAAATAA
1 TAAAA-ATAATATAAAATAA
2477648 ATATATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 10 0.56
22 3 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAATAATATAAAATAAT
Found at i:2477650 original size:11 final size:11
Alignment explanation
Indices: 2477588--2477652 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
2477578 ATTAAGTTAA
2477588 AAATATTAAATAT
1 AAATA-TAAA-AT
* *
2477601 AATTATATAA-
1 AAATATAAAAT
2477611 AAATAATAAAAT
1 AAAT-ATAAAAT
2477623 ATAAT-TAAAAT
1 A-AATATAAAAT
2477634 ATAATATAAAAT
1 A-AATATAAAAT
2477646 AAATATA
1 AAATATA
2477653 TTAATTAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.07
11 23 0.52
12 11 0.25
13 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:2481269 original size:19 final size:19
Alignment explanation
Indices: 2481245--2481303 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 19
2481235 AGATTTTAAT
2481245 TTTTTTAAATTAATTTTTA
1 TTTTTTAAATTAATTTTTA
* *
2481264 TTTTTTACATTGATCATTTTA
1 TTTTTTAAATTAAT--TTTTA
2481285 TTTTATTATAATTACATTT
1 TTTT-TTA-AATTA-ATTT
2481304 AAAAAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 12 0.39
21 9 0.29
22 5 0.16
23 3 0.10
24 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTAATTTTTA
Found at i:2481302 original size:21 final size:19
Alignment explanation
Indices: 2481245--2481303 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
2481235 AGATTTTAAT
2481245 TTTTTTAAATTA-ATTTTTA
1 TTTTTTAAATTACA-TTTTA
*
2481264 TTTTTTACATTGATCATTTTA
1 TTTTTTAAATT-A-CATTTTA
2481285 TTTTATTATAATTACATTT
1 TTTT-TTA-AATTACATTT
2481304 AAAAAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 10 0.30
20 1 0.03
21 14 0.42
22 5 0.15
23 3 0.09
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTACATTTTA
Found at i:2481426 original size:8 final size:8
Alignment explanation
Indices: 2481413--2481442 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2481403 CATTGTTTAA
2481413 AAAATATT
1 AAAATATT
2481421 AAAATATT
1 AAAATATT
2481429 AAAATTATT
1 AAAA-TATT
2481438 AAAAT
1 AAAAT
2481443 TTATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATATT
Found at i:2481601 original size:8 final size:8
Alignment explanation
Indices: 2481588--2481630 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
2481578 TTTATTTTAT
2481588 TTTTAAAA
1 TTTTAAAA
2481596 TTTT-AAA
1 TTTTAAAA
*
2481603 TATTAAAA
1 TTTTAAAA
*
2481611 TATTTATAA
1 T-TTTAAAA
2481620 TTTTAAAA
1 TTTTAAAA
2481628 TTT
1 TTT
2481631 ATATTTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 17 0.59
9 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:2481625 original size:17 final size:15
Alignment explanation
Indices: 2481588--2481630 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
2481578 TTTATTTTAT
2481588 TTTTAAAATTTTAAA
1 TTTTAAAATTTTAAA
*
2481603 TATTAAAATATTTATAA
1 TTTTAAAAT-TTTA-AA
2481620 TTTTAAAATTT
1 TTTTAAAATTT
2481631 ATATTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAATTTTAAA
Found at i:2481875 original size:24 final size:24
Alignment explanation
Indices: 2481848--2481897 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2481838 ATTTTATACG
2481848 ATAAAAATGGATGAAAACAAGAAC
1 ATAAAAATGGATGAAAACAAGAAC
*
2481872 ATAAAAATGGATGATAACAAGAAC
1 ATAAAAATGGATGAAAACAAGAAC
2481896 AT
1 AT
2481898 GAGTCAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (24 bp):
ATAAAAATGGATGAAAACAAGAAC
Found at i:2482302 original size:13 final size:13
Alignment explanation
Indices: 2482284--2482313 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2482274 CCGTCCTGAA
2482284 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
2482297 AAAAAAAAAGAAG
1 AAAAAAAAAAAAG
2482310 AAAA
1 AAAA
2482314 TAAAGGGAAC
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:2488761 original size:11 final size:11
Alignment explanation
Indices: 2488745--2488811 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
2488735 ATTATAAAAA
2488745 ATAATATAAAT
1 ATAATATAAAT
2488756 ATAATATAAAT
1 ATAATATAAAT
*
2488767 AT--TTTAAAT
1 ATAATATAAAT
*
2488776 -TTATATAAATT
1 ATAATATAAA-T
*
2488787 ATATTA-AAAT
1 ATAATATAAAT
* *
2488797 TTTATATAAAT
1 ATAATATAAAT
2488808 ATAA
1 ATAA
2488812 AATGTTTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
8 1 0.02
9 6 0.14
10 9 0.21
11 23 0.55
12 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:2488790 original size:22 final size:22
Alignment explanation
Indices: 2488759--2488807 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
2488749 TATAAATATA
*
2488759 ATATAAA-TAT-TTTAAA-TTT
1 ATATAAATTATATTAAAATTTT
2488778 ATATAAATTATATTAAAATTTT
1 ATATAAATTATATTAAAATTTT
2488800 ATATAAAT
1 ATATAAAT
2488808 ATAAAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 3 0.12
21 5 0.19
22 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAAATTATATTAAAATTTT
Found at i:2488809 original size:28 final size:30
Alignment explanation
Indices: 2488743--2488812 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
2488733 ACATTATAAA
2488743 AAAT-AATATAAATATAATATAAATATTTT
1 AAATAAATATAAATATAATATAAATATTTT
**
2488772 AAATTTATATAAAT-T-ATATTAAA-ATTTT
1 AAATAAATATAAATATAATA-TAAATATTTT
*
2488800 ATATAAATATAAA
1 AAATAAATATAAA
2488813 ATGTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.51
29 9 0.26
30 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATAAATATAAATATAATATAAATATTTT
Found at i:2500899 original size:12 final size:12
Alignment explanation
Indices: 2500882--2500931 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2500872 AATATAATAT
2500882 ATTAATATTAAA
1 ATTAATATTAAA
*
2500894 ATTAATATATATA
1 ATTAATAT-TAAA
2500907 ATTAA-ATTAAA
1 ATTAATATTAAA
*
2500918 AATAAGT-TTAAA
1 ATTAA-TATTAAA
2500930 AT
1 AT
2500932 AATTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 7 0.23
12 16 0.52
13 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
ATTAATATTAAA
Found at i:2500905 original size:24 final size:25
Alignment explanation
Indices: 2500860--2500922 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
2500850 TAATTTATTT
2500860 TTAAA-TAAAAATAATATAATAT-A
1 TTAAATTAAAAATAATATAATATAA
*
2500883 TTAATATTAAAATTAATAT-ATATAA
1 TTAA-ATTAAAAATAATATAATATAA
2500908 TTAAATTAAAAATAA
1 TTAAATTAAAAATAA
2500923 GTTTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 4 0.11
24 15 0.43
25 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAAATTAAAAATAATATAATATAA
Found at i:2501308 original size:13 final size:13
Alignment explanation
Indices: 2501272--2501311 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2501262 TTTTAATTAC
* *
2501272 AAATATTAATTAA
1 AAATATTATTTTA
2501285 AAATATT-TTTTA
1 AAATATTATTTTA
2501297 AAATATTATTTTA
1 AAATATTATTTTA
2501310 AA
1 AA
2501312 TAATAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATATTATTTTA
Found at i:2501643 original size:29 final size:27
Alignment explanation
Indices: 2501602--2501673 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 27
2501592 ATTTTTGAAC
2501602 TTATATTTATCATTCATATA-TTTATTAATA
1 TTATATTT-TCATTCATA-ACTTTA-TAA-A
*
2501632 TTTTATTTTCATTCATAACTTTATAAA
1 TTATATTTTCATTCATAACTTTATAAA
2501659 TTATATTTT-ATTCAT
1 TTATATTTTCATTCAT
2501674 CTATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 6 0.15
27 9 0.23
28 4 0.10
29 13 0.33
30 7 0.18
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATTTTCATTCATAACTTTATAAA
Found at i:2501694 original size:31 final size:31
Alignment explanation
Indices: 2501656--2501720 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
2501646 ATAACTTTAT
2501656 AAATTATATTTTATTCATCTATAA-TTTT-AAA
1 AAATTATA-TTTA-TCATCTATAACTTTTCAAA
*
2501687 AAATTATATTTATCATTTATAACTTTTCAAA
1 AAATTATATTTATCATCTATAACTTTTCAAA
2501718 AAA
1 AAA
2501721 ATTTATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.29
30 8 0.26
31 14 0.45
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTATATTTATCATCTATAACTTTTCAAA
Found at i:2501718 original size:29 final size:27
Alignment explanation
Indices: 2501586--2501718 Score: 90
Period size: 30 Copynumber: 4.6 Consensus size: 27
2501576 TTTATTTTTG
* *
2501586 TTCATAATTTTTGAACTTATATTTATCA
1 TTCATAA-TTTTAAAATTATATTTATCA
* *
2501614 TTCATATATTTATTAATATTTTATTT-TCA
1 TTCATA-A-TT-TTAAAATTATATTTATCA
*
2501643 TTCATAACTTTATAAATTATATTTTATTCA
1 TTCATAATTTTA-AAATTATA-TTTA-TCA
2501673 -TCTATAATTTTAAAAAATTATATTTATCA
1 TTC-ATAATTTT--AAAATTATATTTATCA
*
2501702 TTTATAACTTTTCAAAA
1 TTCATAA-TTTT-AAAA
2501719 AAATTTATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.04
27 7 0.08
28 10 0.12
29 26 0.31
30 29 0.35
31 8 0.10
32 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (27 bp):
TTCATAATTTTAAAATTATATTTATCA
Found at i:2501761 original size:3 final size:3
Alignment explanation
Indices: 2501753--2501785 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2501743 GTTAAAGGTA
*
2501753 AAT AAT AAT AAT AAT AAT AAT ACT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2501786 TCTATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2504725 original size:18 final size:17
Alignment explanation
Indices: 2504698--2504754 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
2504688 ATGTTTAAGG
*
2504698 TTTTTTATATTTATATAA
1 TTTTTAATA-TTATATAA
2504716 TTTTTAATA-TAT-TAA
1 TTTTTAATATTATATAA
2504731 TATTTT-ATATTATATAA
1 T-TTTTAATATTATATAA
*
2504748 ATTTTAA
1 TTTTTAA
2504755 AATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 7 0.21
16 14 0.42
17 4 0.12
18 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAATATTATATAA
Done.