Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 5 of 14
Found at i:935118 original size:2 final size:2
Alignment explanation
Indices: 935111--935144 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
935101 AAAGACCCTA
935111 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
935145 CAAGAAAACC
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):
AT
Found at i:944565 original size:2 final size:2
Alignment explanation
Indices: 944558--944584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
944548 TGCATTCTTT
944558 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 T
944585 TGTTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:951128 original size:14 final size:14
Alignment explanation
Indices: 951109--951136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
951099 TAGAACTGAA
951109 TGGTTACTTTATTC
1 TGGTTACTTTATTC
951123 TGGTTACTTTATTC
1 TGGTTACTTTATTC
951137 CCTATTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TGGTTACTTTATTC
Found at i:952818 original size:4 final size:4
Alignment explanation
Indices: 952805--952881 Score: 102
Period size: 4 Copynumber: 19.5 Consensus size: 4
952795 CAAGTAGAAG
* *
952805 ATAT -TAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
952852 ATGT ATGT ATGT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
952882 GTGTGTATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 3 0.05
4 63 0.95
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (4 bp):
ATAT
Found at i:952820 original size:6 final size:6
Alignment explanation
Indices: 952805--952881 Score: 102
Period size: 6 Copynumber: 13.0 Consensus size: 6
952795 CAAGTAGAAG
* *
952805 ATAT-T ATATAT ATATAT ATATAT ATATAT ATATAT GTATAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
952852 ATGTAT GTATGT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT
952882 GTGTGTATGT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
5 4 0.06
6 59 0.94
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (6 bp):
ATATAT
Found at i:956408 original size:2 final size:2
Alignment explanation
Indices: 956401--956458 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
956391 TTGGATTTAC
956401 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
956443 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
956459 GAAGTACAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:957627 original size:13 final size:13
Alignment explanation
Indices: 957609--957633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
957599 CATCAAGTAG
957609 TTATTTAAATTTT
1 TTATTTAAATTTT
957622 TTATTTAAATTT
1 TTATTTAAATTT
957634 GATTATGATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:957674 original size:20 final size:20
Alignment explanation
Indices: 957636--957674 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
957626 TTAAATTTGA
* *
957636 TTATGATTTATAAATTTATT
1 TTATGATTTAAAAAATTATT
*
957656 TTATTATTTAAAAAATTAT
1 TTATGATTTAAAAAATTAT
957675 AATATTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTATGATTTAAAAAATTATT
Found at i:957708 original size:19 final size:19
Alignment explanation
Indices: 957674--957727 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
957664 TAAAAAATTA
*
957674 TAATATTAAAAATTAT-TTT
1 TAATATT-AAATTTATATTT
957693 TAATATTAATATTTATATTT
1 TAATATTAA-ATTTATATTT
*
957713 TTATAATTAAATTTA
1 TAAT-ATTAAATTTA
957728 AAATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
20 11 0.37
21 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATATTAAATTTATATTT
Found at i:957713 original size:21 final size:20
Alignment explanation
Indices: 957687--957727 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
957677 TATTAAAAAT
957687 TATTTTTA-ATATTAATATTTA
1 TATTTTTATA-ATTAA-ATTTA
957708 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
957728 AAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 13 0.68
22 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTTATAATTAAATTTA
Found at i:957752 original size:21 final size:20
Alignment explanation
Indices: 957674--957724 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
957664 TAAAAAATTA
*
957674 TAATATTAAAAAT-TATTTT
1 TAATATTAAATATATATTTT
*
957693 TAATATTAATATTTATATTTT
1 TAATATTAA-ATATATATTTT
957714 T-ATAATTAAAT
1 TAAT-ATTAAAT
957725 TTAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATTAAATATATATTTT
Found at i:959235 original size:3 final size:3
Alignment explanation
Indices: 959227--959262 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
959217 CAAAGTACAT
*
959227 TTA TTA TTA TAA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
959263 GATGAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:959243 original size:13 final size:13
Alignment explanation
Indices: 959225--959261 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
959215 TTCAAAGTAC
959225 ATTTATTATTATA
1 ATTTATTATTATA
*
959238 ATTTATTATTATT
1 ATTTATTATTATA
959251 A-TTATTATTAT
1 ATTTATTATTAT
959262 TGATGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTATTATTATA
Found at i:959928 original size:16 final size:17
Alignment explanation
Indices: 959904--959936 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
959894 TGTTTTAAAA
959904 AATTATTA-TATATTTT
1 AATTATTATTATATTTT
*
959920 AATTTTTATTATATTTT
1 AATTATTATTATATTTT
959937 TATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTATTATTATATTTT
Found at i:959938 original size:38 final size:36
Alignment explanation
Indices: 959877--959958 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 36
959867 CTTGTAATAA
959877 TTTTTAATTTTTTTTCATGTTTTAAAAA-ATTATTAT
1 TTTTTAATTTTTTTTCATGTTTTAAAAATA-TATTAT
*
959913 ATATTTTAATTTTTATTAT-AT-TTTTATAAATATATTAT
1 -T-TTTTAATTTTT-TT-TCATGTTTTAAAAATATATTAT
959951 TTTTTAAT
1 TTTTTAAT
959959 ATTAAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
36 7 0.17
37 2 0.05
38 25 0.62
39 5 0.12
40 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (36 bp):
TTTTTAATTTTTTTTCATGTTTTAAAAATATATTAT
Found at i:960208 original size:18 final size:18
Alignment explanation
Indices: 960173--960218 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
960163 AATATTTTGA
960173 AATTTAAAATTAAATAA-T
1 AATTT-AAATTAAATAATT
960191 AATTTAAATTAAATTAATT
1 AATTTAAATTAAA-TAATT
960210 AA-TTAAATT
1 AATTTAAATT
960219 TATTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.31
18 15 0.58
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTAAATTAAATAATT
Found at i:960225 original size:14 final size:13
Alignment explanation
Indices: 960192--960230 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
960182 TTAAATAATA
960192 ATTTAAATTAAATT
1 ATTT-AATTAAATT
*
960206 AATTAATTAAATTT
1 ATTTAATTAAA-TT
960220 ATTTAATTAAA
1 ATTTAATTAAA
960231 AGATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAATTAAATT
Found at i:960225 original size:18 final size:18
Alignment explanation
Indices: 960179--960229 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
960169 TTGAAATTTA
960179 AAATTAAA-TAA-TAATTT
1 AAATTAAATTAATTAA-TT
960196 AAATTAAATTAATTAATT
1 AAATTAAATTAATTAATT
* *
960214 AAATTTATTTAATTAA
1 AAATTAAATTAATTAA
960230 AAGATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 19 0.63
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTAAATTAATTAATT
Found at i:960385 original size:22 final size:21
Alignment explanation
Indices: 960360--960401 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
960350 TTTTATATCA
*
960360 TAAAATTTAAATTTATAAATTT
1 TAAAAATTAAATTTA-AAATTT
*
960382 TAAAAATTATATTTAAAATT
1 TAAAAATTAAATTTAAAATT
960402 ATATTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAATTAAATTTAAAATTT
Found at i:960483 original size:10 final size:10
Alignment explanation
Indices: 960463--960499 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
960453 TTAAATCATA
960463 TTAAAATTATT
1 TTAAAA-TATT
960474 TTAAAATATT
1 TTAAAATATT
960484 TT-AAA-ATT
1 TTAAAATATT
960492 TTAAAATA
1 TTAAAATA
960500 AAATTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.21
9 6 0.25
10 7 0.29
11 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTAAAATATT
Found at i:960529 original size:16 final size:16
Alignment explanation
Indices: 960496--960529 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
960486 AAAATTTTAA
* *
960496 AATAAAATTATAATTT
1 AATAAAATTAAAAATT
960512 AATAAAATTAAAAATT
1 AATAAAATTAAAAATT
960528 AA
1 AA
960530 AATTAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAATTAAAAATT
Found at i:963475 original size:22 final size:22
Alignment explanation
Indices: 963447--963488 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
963437 ATTAAAATAT
963447 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
963469 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
963489 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:963499 original size:36 final size:36
Alignment explanation
Indices: 963459--963527 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
963449 TTTTTATATT
* * *
963459 AATATTTAT-ATATTTTTATAATTAAATTTAAATAAA
1 AATATTTATAATATTATTAAAAAT-AATTTAAATAAA
*
963495 AATATTTTTAATATTATTAAAAATAATTTAAAT
1 AATATTTATAATATTATTAAAAATAATTTAAAT
963528 CAATTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 17 0.61
37 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATTTATAATATTATTAAAAATAATTTAAATAAA
Found at i:967558 original size:13 final size:14
Alignment explanation
Indices: 967540--967569 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
967530 AAAAATATTG
967540 TAATTATA-TAAAT
1 TAATTATATTAAAT
967553 TAATTATATTAAAT
1 TAATTATATTAAAT
967567 TAA
1 TAA
967570 ATTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATATTAAAT
Found at i:967768 original size:22 final size:23
Alignment explanation
Indices: 967734--967783 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
967724 TTAAATACTC
*
967734 AAATATAAATTTTAAAT-TTATT
1 AAATATAAATTTTAAATATAATT
* * *
967756 AAATATTATTTTTTAATATAATT
1 AAATATAAATTTTAAATATAATT
967779 AAATA
1 AAATA
967784 AATCAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATAAATTTTAAATATAATT
Found at i:968503 original size:35 final size:35
Alignment explanation
Indices: 968432--968501 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
968422 AATTATTATT
968432 TATTAA-ATAAAATATTTTTAATTAAATTATAAAAA
1 TATTAATATAAAATATTTTT-ATTAAATTATAAAAA
*
968467 TATTAATATAAAATATATTTT-TTAATATTTTAAAA
1 TATTAATATAAAATAT-TTTTATTAA-ATTATAAAA
968502 TAATAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 10 0.32
36 17 0.55
37 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (35 bp):
TATTAATATAAAATATTTTTATTAAATTATAAAAA
Found at i:969061 original size:15 final size:17
Alignment explanation
Indices: 969029--969068 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
969019 ATACAACCCC
*
969029 ATGTAAAAATATATATA
1 ATGTAAAAATATAAATA
969046 AT-TAAAAA-ATAAATA
1 ATGTAAAAATATAAATA
969061 ATGTAAAA
1 ATGTAAAA
969069 TAATTATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
ATGTAAAAATATAAATA
Found at i:969163 original size:19 final size:20
Alignment explanation
Indices: 969124--969163 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
969114 TCGATAATAA
* *
969124 AATTTTGATATAATGTATTT
1 AATTTTAATAAAATGTATTT
969144 AATTTTAATAAAAT-TATTT
1 AATTTTAATAAAATGTATTT
969163 A
1 A
969164 CTATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTTTAATAAAATGTATTT
Found at i:969678 original size:34 final size:33
Alignment explanation
Indices: 969639--969709 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
969629 ATATTATTAT
* * *
969639 AAAAATATTAA-ATTATTTATATTTTAATTTTTTA
1 AAAAATATTAACTTTA-ATATATTAT-ATTTTTTA
969673 AAAAATATTAACTTTAATATATTATATTTTTTA
1 AAAAATATTAACTTTAATATATTATATTTTTTA
969706 AAAA
1 AAAA
969710 TAAAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 12 0.36
34 18 0.55
35 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
AAAAATATTAACTTTAATATATTATATTTTTTA
Found at i:969709 original size:32 final size:32
Alignment explanation
Indices: 969629--969726 Score: 89
Period size: 34 Copynumber: 3.1 Consensus size: 32
969619 AATAAATAAA
* *
969629 ATATTATTATAAAAATATTAAATTATTTATATT
1 ATATT-TTTTAAAAATATTAAATTATATATATT
* *
969662 TTAATTTTTTAAAAAATATTAACTT-TAATATATT
1 AT-ATTTTTT-AAAAATATTAAATTAT-ATATATT
969696 ATATTTTTTAAAAATA--AAA-TAT-TATATT
1 ATATTTTTTAAAAATATTAAATTATATATATT
969724 ATA
1 ATA
969727 ATTAAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
28 9 0.16
29 1 0.02
30 3 0.05
32 7 0.13
33 12 0.22
34 23 0.42
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATTTTTTAAAAATATTAAATTATATATATT
Found at i:969750 original size:49 final size:49
Alignment explanation
Indices: 969692--969792 Score: 109
Period size: 49 Copynumber: 2.0 Consensus size: 49
969682 AACTTTAATA
* *
969692 TATTATATTT-T-TTAAAAATAAAATATTATATTATAATTAAAATTTTAAAT
1 TATTATATTTATAATAAAAAT-AAAT-TTAT-TTAAAATTAAAATTTTAAAT
* *
969742 TATT-TATTTATAAATAAAAATAAATTTATTTAAAATTTATATTTTAAAT
1 TATTATATTTAT-AATAAAAATAAATTTATTTAAAATTAAAATTTTAAAT
969791 TA
1 TA
969793 AATTAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
49 24 0.55
50 9 0.20
51 4 0.09
52 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
TATTATATTTATAATAAAAATAAATTTATTTAAAATTAAAATTTTAAAT
Found at i:969803 original size:49 final size:52
Alignment explanation
Indices: 969704--969807 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 52
969694 TTATATTTTT
* * *
969704 TAAAAATAAAATATTATATTATAATTAAAATTTTAAATTATTTATTTATAAA
1 TAAAAATAAAATATTATATTAAAATTAAAATTTTAAATTAATTATATATAAA
* *
969756 TAAAAAT-AAAT-TTAT-TTAAAATTTATATTTTAAATTAAATTA-ATATAAA
1 TAAAAATAAAATATTATATTAAAATTAAAATTTTAAATT-AATTATATATAAA
969805 TAA
1 TAA
969808 TATTAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 27 0.59
50 8 0.17
51 4 0.09
52 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (52 bp):
TAAAAATAAAATATTATATTAAAATTAAAATTTTAAATTAATTATATATAAA
Found at i:980221 original size:2 final size:2
Alignment explanation
Indices: 980214--980246 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
980204 GAACTCAATG
980214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
980247 CTATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:981129 original size:30 final size:30
Alignment explanation
Indices: 981095--981170 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
981085 TTTTTATTAT
981095 ATTAAAAATTTATTTAAATATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
* *
981125 ATTAAAAATTTATTTAAATGTAAATTAAAG
1 ATTAAAAATTTATTTAAATATAAATTAAAA
*
981155 ATTATAAATTTATTTA
1 ATTAAAAATTTATTTA
981171 TGTATAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAA
Found at i:981654 original size:2 final size:2
Alignment explanation
Indices: 981647--981672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
981637 AAATTTTTGA
981647 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
981673 GATGTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:982650 original size:8 final size:8
Alignment explanation
Indices: 982637--982666 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
982627 TATATCTAAA
982637 TAATTTTT
1 TAATTTTT
982645 TAA-TTTT
1 TAATTTTT
982652 TAATTTTT
1 TAATTTTT
982660 TAATTTT
1 TAATTTT
982667 AATTTATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TAATTTTT
Found at i:982657 original size:15 final size:14
Alignment explanation
Indices: 982637--982671 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
982627 TATATCTAAA
982637 TAATTTTTTAATTTT
1 TAATTTTTTAA-TTT
982652 TAATTTTTTAATTT
1 TAATTTTTTAATTT
982666 TAATTT
1 TAATTT
982672 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TAATTTTTTAATTT
Found at i:983605 original size:20 final size:19
Alignment explanation
Indices: 983582--983632 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
983572 ATTAAATTTT
983582 AATAAAATATTTTTAATTCA
1 AATAAAATATTTTT-ATTCA
*
983602 AATATATAA-ATTTTTATTTA
1 AATA-A-AATATTTTTATTCA
*
983622 AATAACATATT
1 AATAAAATATT
983633 AAATATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 1 0.04
19 4 0.15
20 12 0.46
21 7 0.27
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAAATATTTTTATTCA
Found at i:983951 original size:31 final size:30
Alignment explanation
Indices: 983918--984057 Score: 98
Period size: 27 Copynumber: 4.8 Consensus size: 30
983908 TGTATAACAT
* *
983918 AAATATATAAAAAATAATTAAAATATAATAT
1 AAATATATAAAATAT-ATTAAAATATAATAA
*
983949 AAATAT-TAAAATATTTTTAAATTTATATAATAA
1 AAATATATAAAATA-TATTAAA---ATATAATAA
*
983982 AAAT-TAT-TAATATATTAAAATAT-ATAA
1 AAATATATAAAATATATTAAAATATAATAA
* *
984009 AAATATAT--AATAT-TTTAAATATAATTA
1 AAATATATAAAATATATTAAAATATAATAA
* * *
984036 TAATAAATAAAAT-TATAAAAAT
1 AAATATATAAAATATATTAAAAT
984058 TATGACGTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
26 8 0.09
27 22 0.25
28 8 0.09
29 8 0.09
30 11 0.12
31 13 0.15
32 5 0.06
33 13 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATATATAAAATATATTAAAATATAATAA
Found at i:983956 original size:19 final size:18
Alignment explanation
Indices: 983917--983962 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
983907 ATGTATAACA
983917 TAAATATATAAAAAATAAT
1 TAAA-ATATAAAAAATAAT
983936 TAAAATATAATATAAAT-AT
1 TAAAATATAA-A-AAATAAT
983955 TAAAATAT
1 TAAAATAT
983963 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATAAAAAATAAT
Found at i:984017 original size:10 final size:10
Alignment explanation
Indices: 983918--984018 Score: 55
Period size: 10 Copynumber: 10.0 Consensus size: 10
983908 TGTATAACAT
983918 AAATATATAA
1 AAATATATAA
*
983928 AAA-ATAATTA
1 AAATAT-ATAA
*
983938 AAATATAATAT
1 AAATAT-ATAA
983949 AAATAT-TAA
1 AAATATATAA
* *
983958 AATATTTTTAA
1 AA-ATATATAA
**
983969 ATTTATATAA
1 AAATATATAA
* *
983979 TAAAAAT-TAT
1 -AAATATATAA
* *
983989 TAATATATTA
1 AAATATATAA
983999 AAATATATAA
1 AAATATATAA
984009 AAATATATAA
1 AAATATATAA
984019 TATTTTAAAT
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
9 10 0.15
10 38 0.58
11 18 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATATATAA
Found at i:984019 original size:27 final size:26
Alignment explanation
Indices: 983949--984031 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
983939 AATATAATAT
*
983949 AAATAT-TAAAATATTTTTAA-ATTT-
1 AAATATATAAAA-ATTATTAATATTTA
*
983973 ATATA-ATAAAAATTATTAATATATTA
1 AAATATATAAAAATTATTAATAT-TTA
*
983999 AAATATATAAAAA-TATATAATATTTT
1 AAATATATAAAAATTAT-TAATATTTA
984025 AAATATA
1 AAATATA
984032 ATTATAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.14
24 11 0.22
25 2 0.04
26 16 0.33
27 13 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATATATAAAAATTATTAATATTTA
Found at i:984042 original size:60 final size:60
Alignment explanation
Indices: 983930--984042 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
983920 ATATATAAAA
* *
983930 AATAATTAAAATATAATATAAATATTAAAATATTTTTAAATTTATATAATAAAAATTATT
1 AATAATTAAAATATAATAAAAATATTAAAATATTTTTAAATTAATATAATAAAAATTATT
*
983990 AATATATTAAAATAT-ATAAAAATA-TATAATA-TTTTAAATATAATTATAATAAA
1 AATA-ATTAAAATATAATAAAAATATTAAAATATTTTTAAAT-TAA-TATAATAAA
984043 TAAAATTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 8 0.17
59 8 0.17
60 21 0.45
61 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (60 bp):
AATAATTAAAATATAATAAAAATATTAAAATATTTTTAAATTAATATAATAAAAATTATT
Found at i:984044 original size:15 final size:15
Alignment explanation
Indices: 984024--984057 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
984014 TATAATATTT
*
984024 TAAATATAATTATAA
1 TAAATAAAATTATAA
984039 TAAATAAAATTATAA
1 TAAATAAAATTATAA
984054 -AAAT
1 TAAAT
984058 TATGACGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAAAATTATAA
Found at i:984371 original size:9 final size:9
Alignment explanation
Indices: 984335--984408 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
984325 AAATTTTTTT
984335 TATT-TTTA
1 TATTATTTA
**
984343 TATTAAATA
1 TATTATTTA
984352 T-TTATTTA
1 TATTATTTA
984360 TATTCA-TTA
1 TATT-ATTTA
984369 TA-TATTTA
1 TATTATTTA
984377 TATTATTTA
1 TATTATTTA
984386 TATT-TATTA
1 TATTAT-TTA
*
984395 TATT-TATA
1 TATTATTTA
984403 TATTAT
1 TATTAT
984409 AATTATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 23 0.43
9 29 0.54
10 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (9 bp):
TATTATTTA
Found at i:984424 original size:19 final size:19
Alignment explanation
Indices: 984391--984428 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
984381 ATTTATATTT
*
984391 ATTATATTTATATATTATA
1 ATTATATTTAAATATTATA
984410 ATTATATTTAAATATTATA
1 ATTATATTTAAATATTATA
984429 TATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATATTTAAATATTATA
Found at i:984426 original size:13 final size:15
Alignment explanation
Indices: 984339--984439 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
984329 TTTTTTTATT
984339 TTTATA-TTA-AATA
1 TTTATATTTATAATA
*
984352 -TT-TATTTATATTCA
1 TTTATATTTATAAT-A
*
984366 TTATATATTTATATTA
1 TT-TATATTTATAATA
*
984382 TTTATATTTATTATA
1 TTTATATTTATAATA
984397 TTTATATATTAT-A-A
1 TTTATAT-TTATAATA
984411 -TTATATTTA-AATA
1 TTTATATTTATAATA
*
984424 -TTATATATATAA-A
1 TTTATATTTATAATA
984437 TTT
1 TTT
984440 TGATGAATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
11 2 0.03
12 9 0.12
13 18 0.25
14 6 0.08
15 20 0.27
16 8 0.11
17 10 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATATTTATAATA
Found at i:984469 original size:13 final size:13
Alignment explanation
Indices: 984339--984528 Score: 83
Period size: 13 Copynumber: 13.8 Consensus size: 13
984329 TTTTTTTATT
*
984339 TTTATATTAAATA
1 TTTATATTATATA
984352 TTTAT-TTATATTCA
1 TTTATATTATA-T-A
984366 TTATATATTTATATTA
1 TT-TATA-TTATA-TA
984382 TTTATATTTATTATA
1 TTTATA-TTA-TATA
984397 TTTATA-TATTATA
1 TTTATATTA-TATA
* *
984410 ATTATATT-TAAA
1 TTTATATTATATA
*
984422 TATTATATATATAAA
1 T-TTATAT-TATATA
984437 TTTTGATGAATTA-ATAA
1 -TTT-AT--ATTATAT-A
984454 TTTATATTATATA
1 TTTATATTATATA
984467 TTTTAAAATATTAATATA
1 -TTT---ATATT-ATATA
*
984485 TATATATTAT-T-
1 TTTATATTATATA
984496 TTTATATTATAT-
1 TTTATATTATATA
*
984508 TTTA-ATTAT-TT
1 TTTATATTATATA
984519 TTTATATTAT
1 TTTATATTAT
984529 GTAATTATTA
Statistics
Matches: 146, Mismatches: 7, Indels: 49
0.72 0.03 0.24
Matches are distributed among these distances:
10 1 0.01
11 18 0.12
12 18 0.12
13 31 0.21
14 15 0.10
15 27 0.18
16 12 0.08
17 17 0.12
18 7 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:984503 original size:11 final size:11
Alignment explanation
Indices: 984487--984528 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
984477 TTAATATATA
984487 TATATTATTTT
1 TATATTATTTT
984498 TATATTATATTT
1 TATATTAT-TTT
984510 TA-ATTATTTTT
1 TATATTA-TTTT
984521 TATATTAT
1 TATATTAT
984529 GTAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTATTTT
Found at i:984508 original size:30 final size:30
Alignment explanation
Indices: 984352--984508 Score: 84
Period size: 30 Copynumber: 5.4 Consensus size: 30
984342 ATATTAAATA
* *
984352 TTTAT-TTATATTCAT-TATATATTTATATT
1 TTTATATTATATTAATATATATATAT-TATT
* *
984381 ATTTATATT-TATT-ATATTTATATATTATA
1 -TTTATATTATATTAATATATATATATTATT
* * *
984410 ATTATATT-TA--AATATTATATATATAAAT
1 TTTATATTATATTAATA-TATATATATTATT
* * *
984438 TTT-GATGA-ATTAATA-ATTTATATTATAT
1 TTTATATTATATTAATATATATATATTAT-T
**
984466 ATTT-TAAAATATTAATATATATATATTATT
1 -TTTATATTATATTAATATATATATATTATT
984496 TTTATATTATATT
1 TTTATATTATATT
984509 TTAATTATTT
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
27 14 0.15
28 21 0.22
29 17 0.18
30 31 0.33
31 12 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTATATTATATTAATATATATATATTATT
Found at i:984538 original size:23 final size:22
Alignment explanation
Indices: 984481--984539 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
984471 AAAATATTAA
984481 TATATATATATTA-TTTTTATAT
1 TATATAT-TATTATTTTTTATAT
*
984503 TATATTTTAATTATTTTTTATAT
1 TATATATT-ATTATTTTTTATAT
*
984526 TATGTAATTATTAT
1 TATAT-ATTATTAT
984540 GTCTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.32
23 18 0.58
24 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATATATTATTATTTTTTATAT
Found at i:986381 original size:108 final size:108
Alignment explanation
Indices: 986249--986477 Score: 422
Period size: 108 Copynumber: 2.1 Consensus size: 108
986239 ATGGAGATGA
*
986249 TTCGGCTAGTGATATTGCTAAACACTCTGTTTCAGAAGCTGCTGCTGCCAACTCCAGTGCTAAAC
1 TTCGGCTAGTGATATTGCTAAACACTATGTTTCAGAAGCTGCTGCTGCCAACTCCAGTGCTAAAC
986314 AGAGTGATCAGATTTCTTCTGTCTCTGTCCCTGATAGTAATGG
66 AGAGTGATCAGATTTCTTCTGTCTCTGTCCCTGATAGTAATGG
*
986357 TTCGGCTAGTGATATTGCTAAACACTATGTTTCAGAAGCTGCTGCTGCCGACTCCAGTGCTAAAC
1 TTCGGCTAGTGATATTGCTAAACACTATGTTTCAGAAGCTGCTGCTGCCAACTCCAGTGCTAAAC
*
986422 AGAGTGATGAGATTTCTTCTGTCTCTGTCCCTGATAGTAATGG
66 AGAGTGATCAGATTTCTTCTGTCTCTGTCCCTGATAGTAATGG
*
986465 TTCAGCTAGTGAT
1 TTCGGCTAGTGAT
986478 GGTTCGGCTA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 117 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (108 bp):
TTCGGCTAGTGATATTGCTAAACACTATGTTTCAGAAGCTGCTGCTGCCAACTCCAGTGCTAAAC
AGAGTGATCAGATTTCTTCTGTCTCTGTCCCTGATAGTAATGG
Found at i:987514 original size:3 final size:3
Alignment explanation
Indices: 987506--987530 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
987496 GTGGATCTCT
987506 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
987531 TTTAAGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:991671 original size:14 final size:14
Alignment explanation
Indices: 991652--991681 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
991642 AAAATTATTC
991652 AAATTTATTTAATT
1 AAATTTATTTAATT
*
991666 AAATTTATTTATTT
1 AAATTTATTTAATT
991680 AA
1 AA
991682 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAATTTATTTAATT
Found at i:991675 original size:18 final size:18
Alignment explanation
Indices: 991654--991688 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
991644 AATTATTCAA
*
991654 ATTTATTTAATTAAATTT
1 ATTTATTTAATAAAATTT
991672 ATTTATTTAATAAAATT
1 ATTTATTTAATAAAATT
991689 AAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATTTAATAAAATTT
Found at i:991706 original size:28 final size:29
Alignment explanation
Indices: 991662--991748 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 29
991652 AAATTTATTT
* *
991662 AATTAAATTTATTTATTTAA-TAAAATTA
1 AATTAAATTTATATATTCAATTAAAATTA
*
991690 AATTAAA-TTATCATATTCAATTTAAAATTT
1 AATTAAATTTAT-ATATTCAA-TTAAAATTA
* *
991720 AATT--ATTTATAT-TTTAAGTTCAAATTA
1 AATTAAATTTATATATTCAA-TTAAAATTA
991747 AA
1 AA
991749 ATTTTTACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
27 17 0.35
28 16 0.33
29 4 0.08
30 11 0.23
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (29 bp):
AATTAAATTTATATATTCAATTAAAATTA
Found at i:992131 original size:3 final size:3
Alignment explanation
Indices: 992123--992152 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
992113 TCTATTTAAC
992123 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
992153 TGAAAGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:994256 original size:27 final size:27
Alignment explanation
Indices: 994226--994283 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
994216 CTAAGCATCA
* *
994226 AAATCGAAA-TATAAACCCTAAGGAAAC
1 AAATCGAAACAATAAA-CCTAAGCAAAC
*
994253 AAAT-GAAACAATCAACCTAAGCAAAC
1 AAATCGAAACAATAAACCTAAGCAAAC
994279 AAATC
1 AAATC
994284 CTTACAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.14
Consensus pattern (27 bp):
AAATCGAAACAATAAACCTAAGCAAAC
Found at i:1010615 original size:225 final size:225
Alignment explanation
Indices: 1010224--1010673 Score: 864
Period size: 225 Copynumber: 2.0 Consensus size: 225
1010214 AGGAAACAAT
* *
1010224 AATGAAAATGATAGAAGCTAATACAATTTCAGTTAATGGCTGGTGACATTTAGCTTCTGAGTACG
1 AATGAAAATGATAGAAGCTAATACAATTTCAGTTAATGACTGGTGACATTCAGCTTCTGAGTACG
*
1010289 AAGTGACTGCTTTTTGGACTTAATCAACCAGGTAAAACAAACGCTCATTTGGCATTCTTATTTAG
66 AAGTGACTGCTTTTTGGACTTAATCAACCAGGCAAAACAAACGCTCATTTGGCATTCTTATTTAG
1010354 TTAACAAATGATGCTCTCAGAAAGCAGAAGTTGAATTTTCAAAATGCTATAGTCACACTCACAAA
131 TTAACAAATGATGCTCTCAGAAAGCAGAAGTTGAATTTTCAAAATGCTATAGTCACACTCACAAA
1010419 TCATATACTATTAAATTGATTTTGAATGCA
196 TCATATACTATTAAATTGATTTTGAATGCA
1010449 AATGAAAATGATAGAAGCTAATACAATTTCAGTTAATGACTGGTGACATTCAGCTTCTGAGTACG
1 AATGAAAATGATAGAAGCTAATACAATTTCAGTTAATGACTGGTGACATTCAGCTTCTGAGTACG
*
1010514 AAGTGACTGCTTTTTGGACTTAATCAACCAGGCAAAACAAACGCTCATTTGGCGTTCTTATTTAG
66 AAGTGACTGCTTTTTGGACTTAATCAACCAGGCAAAACAAACGCTCATTTGGCATTCTTATTTAG
1010579 TTAACAAATGATGCTCTCAGAAAGCAGAAGTTGAATTTTCAAAATGCTATAGTCACACTCACAAA
131 TTAACAAATGATGCTCTCAGAAAGCAGAAGTTGAATTTTCAAAATGCTATAGTCACACTCACAAA
1010644 TCATATACTATTAAATTGATTTTGAATGCA
196 TCATATACTATTAAATTGATTTTGAATGCA
1010674 CATGCAGACG
Statistics
Matches: 221, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
225 221 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (225 bp):
AATGAAAATGATAGAAGCTAATACAATTTCAGTTAATGACTGGTGACATTCAGCTTCTGAGTACG
AAGTGACTGCTTTTTGGACTTAATCAACCAGGCAAAACAAACGCTCATTTGGCATTCTTATTTAG
TTAACAAATGATGCTCTCAGAAAGCAGAAGTTGAATTTTCAAAATGCTATAGTCACACTCACAAA
TCATATACTATTAAATTGATTTTGAATGCA
Found at i:1012629 original size:18 final size:18
Alignment explanation
Indices: 1012606--1012640 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1012596 TGATTAATTA
1012606 TTTTATCAAT-TAATTTTT
1 TTTTAT-AATATAATTTTT
1012624 TTTTATAATATAATTTT
1 TTTTATAATATAATTTT
1012641 AAGGTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATATAATTTTT
Found at i:1013123 original size:36 final size:35
Alignment explanation
Indices: 1013062--1013130 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
1013052 TATCGTGTTA
*
1013062 AAAATTTTATTTTATTATTTAAAAAATTAAATATT
1 AAAATTTAATTTTATTATTTAAAAAATTAAATATT
*
1013097 AAAATTTAATTTAATATT-TTTTAAAAATTAAATA
1 AAAATTTAATTT--TATTATTTAAAAAATTAAATA
1013131 AAAATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 11 0.37
36 15 0.50
37 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
AAAATTTAATTTTATTATTTAAAAAATTAAATATT
Found at i:1015044 original size:2 final size:2
Alignment explanation
Indices: 1015037--1015065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1015027 AGTTTTGTTT
1015037 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
1015066 TAAATAAGAA
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:1016139 original size:21 final size:21
Alignment explanation
Indices: 1016115--1016225 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
1016105 TAATAATTTG
*
1016115 TATATTAATATTATATTTTTA
1 TATATTATTATTATATTTTTA
1016136 TATATTATTAATT-TA-TTTTA
1 TATATTATT-ATTATATTTTTA
* *
1016156 TATAAATATTTTTATATTTTTA
1 TAT-ATTATTATTATATTTTTA
* * *
1016178 TTTATAATTTTTATATTGTATTTA
1 TATATTATTATTATA-T-T-TTTA
* *
1016202 TATTTTATTATTA-AATTTTA
1 TATATTATTATTATATTTTTA
1016222 TATA
1 TATA
1016226 AAATTACTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
20 17 0.24
21 28 0.39
22 11 0.15
23 2 0.03
24 13 0.18
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (21 bp):
TATATTATTATTATATTTTTA
Found at i:1016157 original size:18 final size:18
Alignment explanation
Indices: 1016123--1016207 Score: 61
Period size: 18 Copynumber: 4.6 Consensus size: 18
1016113 TGTATATTAA
1016123 TATTATATTTTTATATAT
1 TATTATATTTTTATATAT
*
1016141 TATTA-ATTTATTTTATA-
1 TATTATATTT-TTATATAT
* *
1016158 TA-AATATTTTTATATTTT
1 TATTATATTTTTATA-TAT
1016176 TATTTATAATTTTTATAT-T
1 TA-TTAT-ATTTTTATATAT
1016195 GTATTTATATTTT
1 -TA-TTATATTTT
1016208 ATTATTAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
16 5 0.09
17 11 0.20
18 13 0.24
19 6 0.11
20 10 0.19
21 9 0.17
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (18 bp):
TATTATATTTTTATATAT
Found at i:1016199 original size:20 final size:20
Alignment explanation
Indices: 1016161--1016207 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1016151 TTTTATATAA
*
1016161 ATATTTTTATATTTTTATTT
1 ATATTTTTATATTTGTATTT
1016181 ATAATTTTTATA-TTGTATTT
1 AT-ATTTTTATATTTGTATTT
1016201 ATATTTT
1 ATATTTT
1016208 ATTATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
ATATTTTTATATTTGTATTT
Found at i:1016203 original size:11 final size:11
Alignment explanation
Indices: 1016125--1016210 Score: 56
Period size: 11 Copynumber: 8.1 Consensus size: 11
1016115 TATATTAATA
1016125 TTATATTTT-T
1 TTATATTTTAT
* *
1016135 ATATATTATTAA
1 TTATATT-TTAT
1016147 TT-TATTTTAT
1 TTATATTTTAT
* * *
1016157 ATAAATATT-T
1 TTATATTTTAT
1016167 TTATATTTTTAT
1 TTATA-TTTTAT
*
1016179 TTATA-ATT-T
1 TTATATTTTAT
*
1016188 TTATATTGTAT
1 TTATATTTTAT
1016199 TTATATTTTAT
1 TTATATTTTAT
1016210 T
1 T
1016211 ATTAAATTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
9 6 0.11
10 17 0.31
11 25 0.45
12 7 0.13
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (11 bp):
TTATATTTTAT
Found at i:1017112 original size:9 final size:9
Alignment explanation
Indices: 1017098--1017136 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
1017088 TATTATGGTA
1017098 AAATATTAT
1 AAATATTAT
1017107 AAATATTAT
1 AAATATTAT
1017116 AAATATTAT
1 AAATATTAT
1017125 AAATATTA-
1 AAATATTAT
1017133 AAAT
1 AAAT
1017137 TTAAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATATTAT
Found at i:1017219 original size:15 final size:16
Alignment explanation
Indices: 1017186--1017227 Score: 68
Period size: 15 Copynumber: 2.6 Consensus size: 16
1017176 AACATTACTA
1017186 TTAAAAAAACTTTTGAG
1 TTAAAAAAA-TTTTGAG
1017203 TTAAAAAAATTTT-AG
1 TTAAAAAAATTTTGAG
1017218 TTAAAAAAAT
1 TTAAAAAAAT
1017228 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 12 0.48
16 4 0.16
17 9 0.36
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (16 bp):
TTAAAAAAATTTTGAG
Found at i:1017235 original size:14 final size:15
Alignment explanation
Indices: 1017186--1017238 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1017176 AACATTACTA
*
1017186 TTAAAAAAACTTTTGAG
1 TTAAAAAAA-TTAT-AG
*
1017203 TTAAAAAAATTTTAG
1 TTAAAAAAATTATAG
*
1017218 TTAAAAAAA-TATAT
1 TTAAAAAAATTATAG
1017232 TTAAAAA
1 TTAAAAA
1017239 GTATGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 10 0.29
15 11 0.32
16 4 0.12
17 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (15 bp):
TTAAAAAAATTATAG
Found at i:1027397 original size:15 final size:15
Alignment explanation
Indices: 1027377--1027407 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1027367 TAATATTTGC
1027377 TACTACTTGATTGTA
1 TACTACTTGATTGTA
1027392 TACTACTTGATTGTA
1 TACTACTTGATTGTA
1027407 T
1 T
1027408 CCATGTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TACTACTTGATTGTA
Found at i:1029899 original size:32 final size:32
Alignment explanation
Indices: 1029856--1029937 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
1029846 ATAAAAAAAT
** * *
1029856 AAAAATCATTACAAACGTTTAATATTAT-AAA
1 AAAAATCATTACAAACACTCAAAATTATCAAA
1029887 AAATAATCATTACAAACACTCAAAATTATCGAAA
1 AAA-AATCATTACAAACACTCAAAATTATC-AAA
1029921 AAAAATCATTACAAACA
1 AAAAATCATTACAAACA
1029938 TCGCAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 21 0.48
33 14 0.32
34 6 0.14
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (32 bp):
AAAAATCATTACAAACACTCAAAATTATCAAA
Found at i:1029946 original size:33 final size:33
Alignment explanation
Indices: 1029884--1029952 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
1029874 TTAATATTAT
1029884 AAAAAATAATCATTACAAACACTCAAAATTATCG
1 AAAAAATAATCATTACAAACACTCAAAATTA-CG
*
1029918 AAAAAA-AATCATTACAAACA-TCGCAAATTACG
1 AAAAAATAATCATTACAAACACTC-AAAATTACG
1029950 AAA
1 AAA
1029953 CACAAAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 7 0.21
33 20 0.61
34 6 0.18
ACGTcount: A:0.58, C:0.17, G:0.04, T:0.20
Consensus pattern (33 bp):
AAAAAATAATCATTACAAACACTCAAAATTACG
Found at i:1031929 original size:2 final size:2
Alignment explanation
Indices: 1031924--1031953 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1031914 TTTTTTTTTT
*
1031924 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1031954 AGGTGCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1036267 original size:14 final size:14
Alignment explanation
Indices: 1036248--1036281 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1036238 CACCGCCTTT
1036248 CTCTCCCCCTCTCC
1 CTCTCCCCCTCTCC
*
1036262 CTCTCCCTCTCTCC
1 CTCTCCCCCTCTCC
1036276 CTCTCC
1 CTCTCC
1036282 TCCATCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (14 bp):
CTCTCCCCCTCTCC
Found at i:1038043 original size:20 final size:21
Alignment explanation
Indices: 1038002--1038063 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
1037992 GATTAAGCTT
1038002 AATAAAATATAA-AT-TTAATA
1 AATAAAATATAATATATT-ATA
1038022 AATAAAATATAATATATT-TA
1 AATAAAATATAATATATTATA
1038042 AA-AATAAT-TAATATA--ATA
1 AATAA-AATATAATATATTATA
1038060 AATA
1 AATA
1038064 TTACATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.11
19 10 0.27
20 19 0.51
21 2 0.05
22 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAATATAATATATTATA
Found at i:1038063 original size:9 final size:9
Alignment explanation
Indices: 1038001--1038064 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
1037991 TGATTAAGCT
1038001 TAATAAA-A
1 TAATAAATA
*
1038009 T-ATAAATT
1 TAATAAATA
1038017 TAATAAATA
1 TAATAAATA
*
1038026 AAATATAATA
1 TAATA-AATA
* *
1038036 TATTTAAAAA
1 TA-ATAAATA
*
1038046 TAATTAATA
1 TAATAAATA
1038055 TAATAAATA
1 TAATAAATA
1038064 T
1 T
1038065 TACATAATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 23 0.55
10 10 0.24
11 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATAAATA
Found at i:1038154 original size:17 final size:17
Alignment explanation
Indices: 1038092--1038157 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
1038082 ATTATATTTT
*
1038092 TTATTTAAAATAT-TAA
1 TTATTAAAAATATATAA
*
1038108 TATATTAAAAAAATTATAA
1 T-TATTAAAAATA-TATAA
**
1038127 TTA-T--ATTTATATAA
1 TTATTAAAAATATATAA
1038141 TTATTAAAAATATATAA
1 TTATTAAAAATATATAA
1038158 AATATGATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 11
0.67 0.13 0.20
Matches are distributed among these distances:
14 8 0.22
15 3 0.08
16 1 0.03
17 18 0.49
18 3 0.08
19 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATTAAAAATATATAA
Found at i:1038181 original size:98 final size:93
Alignment explanation
Indices: 1038004--1038181 Score: 207
Period size: 93 Copynumber: 1.9 Consensus size: 93
1037994 TTAAGCTTAA
* * *
1038004 TAAAATATAAATTTAATAAATAAAATATAATATATTTAAAAATAATTAATATAATAAATATTACA
1 TAAAATATAAATATAATAAATAAAATATAATATATTTAAAAATAATTAAAATAATAAATATGACA
1038069 TAATTATATATTTATTATATTTTTTATT
66 TAATTATATATTTATTATATTTTTTATT
* * * *
1038097 TAAAATATTAATATATTAAA-AAAATTATAATTATATTTATATAATTATTAAAAATATATAAAAT
1 TAAAATATAAATATAATAAATAAAA-TATAA-TATATTTA-AAAATAATT-AAAATA-AT-AAAT
*
1038161 ATGATATAAATTAT-TATTTAT
60 ATGACAT-AATTATATATTTAT
1038182 AACAGTTTGA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
92 4 0.06
93 22 0.31
94 8 0.11
95 7 0.10
96 5 0.07
97 2 0.03
98 16 0.23
99 6 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (93 bp):
TAAAATATAAATATAATAAATAAAATATAATATATTTAAAAATAATTAAAATAATAAATATGACA
TAATTATATATTTATTATATTTTTTATT
Found at i:1038913 original size:22 final size:22
Alignment explanation
Indices: 1038883--1038935 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1038873 TTTATCAAAA
*
1038883 TTTAT-ATTAATATTTATAT-AT
1 TTTATAATTAA-ATTTAAATAAT
1038904 TTTATAATTAAATTTAAATAAT
1 TTTATAATTAAATTTAAATAAT
*
1038926 TTTTTAATTA
1 TTTATAATTA
1038936 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATAATTAAATTTAAATAAT
Found at i:1039933 original size:28 final size:27
Alignment explanation
Indices: 1039876--1039933 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
1039866 TAATCGTTTC
*
1039876 ATTATTTAAATATATTAATAATTTTAT
1 ATTAATTAAATATATTAATAATTTTAT
1039903 ATTAATTAAATAATAATTAA-AATTTTAT
1 ATTAATTAAAT-AT-ATTAATAATTTTAT
1039931 ATT
1 ATT
1039934 TCAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 10 0.36
28 13 0.46
29 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAATTAAATATATTAATAATTTTAT
Found at i:1043007 original size:2 final size:2
Alignment explanation
Indices: 1043000--1043030 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1042990 TTTTGAAAGA
1043000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1043031 GAAATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1043316 original size:2 final size:2
Alignment explanation
Indices: 1043309--1043333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1043299 GTTTTTCTTT
1043309 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 T
1043334 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1043369 original size:2 final size:2
Alignment explanation
Indices: 1043333--1043357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1043323 TATATATATA
1043333 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1043358 ATTGGGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1043753 original size:25 final size:24
Alignment explanation
Indices: 1043725--1043771 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1043715 TTAAACTGTC
1043725 AAATTAAATAAATAATTC-GATTCAT
1 AAATTAAA-AAA-AATTCTGATTCAT
1043750 AAATTAAAAAAAATTCTGATTC
1 AAATTAAAAAAAATTCTGATTC
1043772 TTTAAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 8 0.38
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATTAAAAAAAATTCTGATTCAT
Found at i:1044670 original size:2 final size:2
Alignment explanation
Indices: 1044663--1044693 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1044653 ATAATATTCT
1044663 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
1044694 GTAAAAGCAA
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:1044901 original size:13 final size:13
Alignment explanation
Indices: 1044883--1044907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1044873 ATGACGTATT
1044883 TTTAAATTAAATA
1 TTTAAATTAAATA
1044896 TTTAAATTAAAT
1 TTTAAATTAAAT
1044908 TTAAATTTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATTAAATA
Found at i:1045918 original size:2 final size:2
Alignment explanation
Indices: 1045913--1045945 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1045903 GAAAAAAGAA
*
1045913 AT AT AT AT AT CT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1045946 TTGCATGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1049382 original size:4 final size:4
Alignment explanation
Indices: 1049373--1049400 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1049363 CTTCAAATAG
1049373 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1049401 CTTGAGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1049779 original size:21 final size:21
Alignment explanation
Indices: 1049739--1049778 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1049729 TTTACATTGA
1049739 TTTTGAAAGTAAAATATTTTC
1 TTTTGAAAGTAAAATATTTTC
*
1049760 TTTT-AAATTAAAATATTTT
1 TTTTGAAAGTAAAATATTTT
1049779 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTGAAAGTAAAATATTTTC
Found at i:1056712 original size:12 final size:12
Alignment explanation
Indices: 1056697--1056724 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1056687 TGTTTTGGTT
1056697 TTTGTCTTTGTC
1 TTTGTCTTTGTC
1056709 TTTGTCTTTGTC
1 TTTGTCTTTGTC
1056721 TTTG
1 TTTG
1056725 ACTTGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTGTCTTTGTC
Found at i:1060637 original size:17 final size:16
Alignment explanation
Indices: 1060617--1060704 Score: 57
Period size: 13 Copynumber: 5.9 Consensus size: 16
1060607 AACAAAAAAT
1060617 ATAAATATATTTATTTA
1 ATAAATATATTTA-TTA
* *
1060634 ATAATTAAATTTA--A
1 ATAAATATATTTATTA
*
1060648 ATAAA-ATATATATT-
1 ATAAATATATTTATTA
* *
1060662 -TAAATACATTTATTC
1 ATAAATATATTTATTA
*
1060677 ATAAATATATTT-GT-
1 ATAAATATATTTATTA
1060691 AT-AATATATTTATT
1 ATAAATATATTTATT
1060705 TTCGAATAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
13 18 0.33
14 15 0.27
15 1 0.02
16 10 0.18
17 11 0.20
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (16 bp):
ATAAATATATTTATTA
Found at i:1060972 original size:14 final size:15
Alignment explanation
Indices: 1060941--1060973 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1060931 AATAAATAAA
1060941 TTTAAATATTTTAAT
1 TTTAAATATTTTAAT
1060956 TTTAAAT-TTTTAAT
1 TTTAAATATTTTAAT
1060970 TTTA
1 TTTA
1060974 TGTAGTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAAATATTTTAAT
Found at i:1077088 original size:13 final size:13
Alignment explanation
Indices: 1077070--1077095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1077060 CGACTGGAAA
1077070 CAGAAATTGCATT
1 CAGAAATTGCATT
1077083 CAGAAATTGCATT
1 CAGAAATTGCATT
1077096 TTAAGGTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAGAAATTGCATT
Found at i:1083254 original size:15 final size:14
Alignment explanation
Indices: 1083203--1083251 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1083193 GTAAATGATG
*
1083203 TATTTTAATTTTTA
1 TATTTTAAATTTTA
* *
1083217 TAATATTAAATTTAA
1 T-ATTTTAAATTTTA
*
1083232 TATTTTAACTTTTA
1 TATTTTAAATTTTA
1083246 TATTTT
1 TATTTT
1083252 TAAAATTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTAAATTTTA
Found at i:1094122 original size:24 final size:25
Alignment explanation
Indices: 1094087--1094137 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1094077 TTTTGAGATA
*
1094087 TTTTATGAATTAA-AAAAAGTTATT
1 TTTTATGAATTAATAAAAAGATATT
*
1094111 TTTTAT-ATATTAATAATAAGATATT
1 TTTTATGA-ATTAATAAAAAGATATT
1094136 TT
1 TT
1094138 AATTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 11 0.48
25 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTATGAATTAATAAAAAGATATT
Found at i:1094502 original size:5 final size:5
Alignment explanation
Indices: 1094492--1094535 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
1094482 TGGCTTGCAT
*
1094492 TTATA TTATA TTATA TTATA TTTTA TTATA TATATA TATATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA TT
1094536 TATCTCATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 25 0.69
6 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:1095110 original size:29 final size:30
Alignment explanation
Indices: 1095041--1095110 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 30
1095031 ATAAAAAACC
* *
1095041 AATACA-ATA-AATATTATATGATATATTT
1 AATACATATATAATATAATATGATATAATT
*
1095069 AA-ACATA-ATTAATATAATATG-TTTAATT
1 AATACATATA-TAATATAATATGATATAATT
1095097 AATACATATATAAT
1 AATACATATATAAT
1095111 TTATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
27 4 0.12
28 10 0.29
29 19 0.56
30 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (30 bp):
AATACATATATAATATAATATGATATAATT
Found at i:1104909 original size:2 final size:2
Alignment explanation
Indices: 1104902--1104930 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1104892 CCATGTCACT
1104902 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
1104931 GTAAAAGCCT
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:1105741 original size:29 final size:32
Alignment explanation
Indices: 1105700--1105761 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 32
1105690 ATAAAAAATT
*
1105700 AATATAATAAATAT-TTTATA-ATAT-ATTTA
1 AATATAATAAATATAATTATATATATAATTTA
* *
1105729 AATATGATTAATATAATTATATATATAATTTA
1 AATATAATAAATATAATTATATATATAATTTA
1105761 A
1 A
1105762 TACACAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 5 0.19
31 4 0.15
32 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
AATATAATAAATATAATTATATATATAATTTA
Found at i:1118224 original size:19 final size:19
Alignment explanation
Indices: 1118200--1118236 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1118190 ATGAGCTTTT
*
1118200 ATTTTTTATATTAAAATTG
1 ATTTTTTATAATAAAATTG
1118219 ATTTTTTATAATAAAATT
1 ATTTTTTATAATAAAATT
1118237 AAAGTATGAA
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:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTTTATAATAAAATTG
Found at i:1121188 original size:2 final size:2
Alignment explanation
Indices: 1121181--1121215 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1121171 CAATAGAATT
1121181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1121216 ACACCTAAAA
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:1121402 original size:5 final size:5
Alignment explanation
Indices: 1121392--1121418 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1121382 CATTTTCAAG
1121392 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1121419 CAGCTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1122702 original size:24 final size:23
Alignment explanation
Indices: 1122674--1122718 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1122664 TTTTTATTTT
* *
1122674 TTTAATTTGTATTTAAAATATGTA
1 TTTAATATATATTT-AAATATGTA
1122698 TTTAATATATATTTAAATATG
1 TTTAATATATATTTAAATATG
1122719 AATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTAATATATATTTAAATATGTA
Found at i:1122704 original size:11 final size:12
Alignment explanation
Indices: 1122681--1122718 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1122671 TTTTTTAATT
1122681 TGTATTTAAAATA
1 TGTATTT-AAATA
1122694 TGTATTT-AATA
1 TGTATTTAAATA
*
1122705 TATATTTAAATA
1 TGTATTTAAATA
1122717 TG
1 TG
1122719 AATATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 5 0.23
13 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TGTATTTAAATA
Found at i:1123471 original size:29 final size:30
Alignment explanation
Indices: 1123428--1123486 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1123418 AAAATTAATC
* *
1123428 AAATATTATATAATACAAAAAAATA-ATAA
1 AAATATTAAAAAATACAAAAAAATATATAA
**
1123457 AAATATTAAAAAATATTAAAAAATATATAA
1 AAATATTAAAAAATACAAAAAAATATATAA
1123487 TATAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (30 bp):
AAATATTAAAAAATACAAAAAAATATATAA
Found at i:1123500 original size:13 final size:12
Alignment explanation
Indices: 1123477--1123514 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1123467 AAATATTAAA
1123477 AAATATATAATAT
1 AAAT-TATAATAT
1123490 AAATTATTAATAT
1 AAATTA-TAATAT
1123503 -AATTATAATAT
1 AAATTATAATAT
1123514 A
1 A
1123515 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 7 0.30
13 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTATAATAT
Found at i:1123523 original size:19 final size:21
Alignment explanation
Indices: 1123501--1123546 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
1123491 AATTATTAAT
1123501 ATAATTAT-AATATAT-AAAA
1 ATAATTATAAATATATGAAAA
* *
1123520 ATAA-AATAAATATATGAATA
1 ATAATTATAAATATATGAAAA
1123540 ATAATTA
1 ATAATTA
1123547 AGTAAACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
20 7 0.33
21 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAATTATAAATATATGAAAA
Found at i:1123863 original size:31 final size:31
Alignment explanation
Indices: 1123825--1123887 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1123815 ACTCAACCTG
*
1123825 TCCAAGAAAATCAGCATGAACAGACTGCTAT
1 TCCAAGAAAATCAGCATGAACAGACTGATAT
*
1123856 TCCAAGAAAATCAGTATGAACAGACTGATAT
1 TCCAAGAAAATCAGCATGAACAGACTGATAT
1123887 T
1 T
1123888 AAAATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (31 bp):
TCCAAGAAAATCAGCATGAACAGACTGATAT
Found at i:1124308 original size:17 final size:17
Alignment explanation
Indices: 1124288--1124336 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1124278 TAAATTATTA
1124288 TTTAATTAATAATAAAT
1 TTTAATTAATAATAAAT
* *
1124305 TTTATTTAATTATAAAT
1 TTTAATTAATAATAAAT
*
1124322 ATTAA-TAA-AATAAAT
1 TTTAATTAATAATAAAT
1124337 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 18 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATTAATAATAAAT
Found at i:1124309 original size:21 final size:21
Alignment explanation
Indices: 1124265--1124316 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1124255 AATTAAATAG
*
1124265 ATTTAATTTAATTTAAATTATT
1 ATTTAA-TTAATATAAATTATT
1124287 ATTTAATTAATAATAAATT-TT
1 ATTTAATTAAT-ATAAATTATT
1124308 ATTTAATTA
1 ATTTAATTA
1124317 TAAATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTAATATAAATTATT
Found at i:1124322 original size:21 final size:22
Alignment explanation
Indices: 1124265--1124322 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1124255 AATTAAATAG
*
1124265 ATTTAATT-TAATTTAAATTATT
1 ATTTAATTATAA-ATAAATTATT
1124287 ATTTAATTA-ATAATAAATT-TT
1 ATTTAATTATA-AATAAATTATT
1124308 ATTTAATTATAAATA
1 ATTTAATTATAAATA
1124323 TTAATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 15 0.47
22 16 0.50
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTAATTATAAATAAATTATT
Found at i:1125964 original size:22 final size:23
Alignment explanation
Indices: 1125906--1125965 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
1125896 TAATTGAGCT
* * *
1125906 TTTAA-TTTAAGTTTAGATGAAT
1 TTTAAGTTTAAATTTAAATGAAG
* *
1125928 TTTTAGTTTAGATTTAAATG-AG
1 TTTAAGTTTAAATTTAAATGAAG
1125950 TTTAAGTTTAAATTTA
1 TTTAAGTTTAAATTTA
1125966 TATTTTATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (23 bp):
TTTAAGTTTAAATTTAAATGAAG
Found at i:1128674 original size:46 final size:46
Alignment explanation
Indices: 1128612--1128707 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
1128602 CATATAGATT
1128612 ATAAGTTTAAGTGAATATCATTGCTTAAAAAAACCAAAATTATATA
1 ATAAGTTTAAGTGAATATCATTGCTTAAAAAAACCAAAATTATATA
1128658 ATAAGTTTAAGTGAATATCATTGCTTAAAAAAACCAAAATTATATA
1 ATAAGTTTAAGTGAATATCATTGCTTAAAAAAACCAAAATTATATA
1128704 ATAA
1 ATAA
1128708 TAAATATAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (46 bp):
ATAAGTTTAAGTGAATATCATTGCTTAAAAAAACCAAAATTATATA
Found at i:1129945 original size:18 final size:18
Alignment explanation
Indices: 1129885--1129949 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 18
1129875 AATATGTTAT
*
1129885 AAAA-AATAT-ATATATA
1 AAAATAATATAATACATA
* *
1129901 AAAAT-TTATATTACATA
1 AAAATAATATAATACATA
*
1129918 AATTATTAATATAATACATA
1 AA--AATAATATAATACATA
1129938 AAAATAATATAA
1 AAAATAATATAA
1129950 ATATATTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 9 0.24
19 2 0.05
20 12 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAATATAATACATA
Found at i:1130807 original size:22 final size:22
Alignment explanation
Indices: 1130739--1130807 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
1130729 GACAAGTTCA
* * *
1130739 TATTTTCATGCTGTGTTCATAT
1 TATTTTTATGTTGTGTTCTTAT
1130761 TATTTTTATGTTGTGTT-TTAAT
1 TATTTTTATGTTGTGTTCTT-AT
1130783 TATTTTTATTATGTTGTGTTCTTAT
1 TA--TTT-TTATGTTGTGTTCTTAT
1130808 CATGTCTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 19 0.49
24 3 0.08
25 14 0.36
26 2 0.05
ACGTcount: A:0.17, C:0.06, G:0.13, T:0.64
Consensus pattern (22 bp):
TATTTTTATGTTGTGTTCTTAT
Found at i:1132220 original size:17 final size:17
Alignment explanation
Indices: 1132195--1132233 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1132185 AACAAATAAA
1132195 TATTATTTAATAAAATT
1 TATTATTTAATAAAATT
* *
1132212 TATTTTTTATTAAAATT
1 TATTATTTAATAAAATT
*
1132229 AATTA
1 TATTA
1132234 AAAATATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTTAATAAAATT
Found at i:1132368 original size:21 final size:21
Alignment explanation
Indices: 1132344--1132401 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
1132334 TTAATAAAAT
*
1132344 TTAATTATAAATTAAATTTTA
1 TTAATTATAAATTAAAATTTA
*
1132365 TTAATAAT-AATTAAAATTTA
1 TTAATTATAAATTAAAATTTA
* * *
1132385 TAAATTAAAAATAAAAA
1 TTAATTATAAATTAAAA
1132402 GACTCTAGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAATTATAAATTAAAATTTA
Found at i:1132707 original size:6 final size:6
Alignment explanation
Indices: 1132696--1132724 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1132686 CCTAGCCCAG
1132696 CGCCAC CGCCAC CGCCAC CGCCAC CGCCA
1 CGCCAC CGCCAC CGCCAC CGCCAC CGCCA
1132725 TCTACACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.66, G:0.17, T:0.00
Consensus pattern (6 bp):
CGCCAC
Found at i:1134467 original size:16 final size:15
Alignment explanation
Indices: 1134425--1134470 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
1134415 TATCTTTATT
1134425 TAAATA-TAATAAATA
1 TAAATATTAA-AAATA
1134440 TAAATATTAAAAATA
1 TAAATATTAAAAATA
*
1134455 TATAATTTTAAAAATA
1 TA-AATATTAAAAATA
1134471 AAAAACTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATTAAAAATA
Found at i:1137800 original size:2 final size:2
Alignment explanation
Indices: 1137795--1137824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1137785 ACACACGCGC
1137795 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
1137825 GTCATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.