Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:2646710 original size:31 final size:32
Alignment explanation
Indices: 2646670--2646740 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2646660 AAATATAAAC
* * *
2646670 ATAACATAAA-TATAAACGTGTTGAAATTTAT
1 ATAAAATAAATTATAAACATGTTAAAATTTAT
* * *
2646701 ATAAAATAAATTATTAATATGTTAAAATTTGT
1 ATAAAATAAATTATAAACATGTTAAAATTTAT
2646733 ATAAAATA
1 ATAAAATA
2646741 TATAACACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (32 bp):
ATAAAATAAATTATAAACATGTTAAAATTTAT
Found at i:2647197 original size:204 final size:205
Alignment explanation
Indices: 2646847--2647449 Score: 940
Period size: 204 Copynumber: 2.9 Consensus size: 205
2646837 CAATTCCCTA
* ** *
2646847 ATAGGATTGCTTTAATAAATAGTTTATAGAAGTTTAAAGATTTATAGATAAAGCATTATGACTTT
1 ATAGGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
2646912 TGCATTGATAATCCCCTTGGCAATCAAAGAAAGACTTTTTTTTTAAGGAAAAAAAA-TATTTTTA
66 TGCATTGATAATCCCCTTGGCAATCAAAGAAAGACTTTTTTTTTAAGGAAAAAAAAGTATTTTTA
2646976 TACACATTTTACGACATTATGATTTTACTTTGAATTTATTCATACTTCGATTATTATTAAATAAA
131 TACACATTTTACGACATTATGATTTTACTTTGAATTTATTCATACTTCGATTATTATTAAATAAA
2647041 ATGATTTACT
196 ATGATTTACT
2647051 ATAGGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
1 ATAGGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
2647116 TGCATTGATAATCCCCTTGGCAATCAAAGAAAGACTTTTTTTTTAA-GAAAAAAAAGTATTTTTA
66 TGCATTGATAATCCCCTTGGCAATCAAAGAAAGACTTTTTTTTTAAGGAAAAAAAAGTATTTTTA
* *
2647180 TACACATTTTACGACATTATGATTTTGCTTTGAATTTATTCATACTTCGATTATTATTAGATAAA
131 TACACATTTTACGACATTATGATTTTACTTTGAATTTATTCATACTTCGATTATTATTAAATAAA
2647245 ATGATTTACT
196 ATGATTTACT
*
2647255 ATAAGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
1 ATAGGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
* * * * *
2647320 TGGATTGATAATTCTCTTGGCAATCAAAGGAGGACTTTTTTAAAAGAAAATTTTAAGGAAAAAAA
66 TGCATTGATAATCCCCTTGGCAATCAAAGAAAGAC-TTTTT---------TTTTAAGG-AAAAAA
* * * * *
2647385 AAGTATTTTTATAAACATTTTATGACATTATGATTTTACTTTAAATTTATTCATAATTTGATTAT
120 AAGTATTTTTATACACATTTTACGACATTATGATTTTACTTTGAATTTATTCATACTTCGATTAT
2647450 AAGAAATAAT
Statistics
Matches: 368, Mismatches: 18, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
203 9 0.02
204 282 0.77
205 5 0.01
214 6 0.02
215 1 0.00
216 65 0.18
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (205 bp):
ATAGGATTGCTTTAATATATAGTTTATAGAAGTTTATGGATTTATAGATAAGGCATTATGACTTT
TGCATTGATAATCCCCTTGGCAATCAAAGAAAGACTTTTTTTTTAAGGAAAAAAAAGTATTTTTA
TACACATTTTACGACATTATGATTTTACTTTGAATTTATTCATACTTCGATTATTATTAAATAAA
ATGATTTACT
Found at i:2647701 original size:19 final size:19
Alignment explanation
Indices: 2647677--2647715 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2647667 TATTTCTAAC
2647677 TTTTTAAAATTTTATAAAT
1 TTTTTAAAATTTTATAAAT
* * *
2647696 TTTTTATATTTTTATTAAT
1 TTTTTAAAATTTTATAAAT
2647715 T
1 T
2647716 AAATCGATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAAAATTTTATAAAT
Found at i:2648915 original size:19 final size:19
Alignment explanation
Indices: 2648873--2648908 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2648863 TTCTAATCTT
2648873 TTTAAACATTGAACAAATC
1 TTTAAACATTGAACAAATC
2648892 TTTAAAC-TTGAACAAAT
1 TTTAAACATTGAACAAAT
2648909 AACTTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (19 bp):
TTTAAACATTGAACAAATC
Found at i:2649089 original size:19 final size:21
Alignment explanation
Indices: 2649065--2649113 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
2649055 TGTTAAAAAA
2649065 ATATTAAAATAT-TAT-TTTT
1 ATATTAAAATATATATATTTT
* *
2649084 ATATTAATATTTATATATTTT
1 ATATTAAAATATATATATTTT
2649105 ATAATTAAA
1 AT-ATTAAA
2649114 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAATATATATATTTT
Found at i:2651219 original size:3 final size:3
Alignment explanation
Indices: 2651211--2651250 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2651201 TTTGTGATTG
2651211 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2651251 TTGTAACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2651584 original size:15 final size:15
Alignment explanation
Indices: 2651545--2651628 Score: 68
Period size: 15 Copynumber: 5.8 Consensus size: 15
2651535 ATATTGATAT
2651545 TTAAAATTTATTTT-
1 TTAAAATTTATTTTA
* *
2651559 TTTATATTTATTTTA
1 TTAAAATTTATTTTA
2651574 TTAAAATTTATTTTA
1 TTAAAATTTATTTTA
* *
2651589 CTATAATTT-TTTTA
1 TTAAAATTTATTTTA
** *
2651603 GCCAAAA-TTCTTTT-
1 -TTAAAATTTATTTTA
2651617 TTAAAATTTATT
1 TTAAAATTTATT
2651629 AATATATTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
13 4 0.07
14 23 0.42
15 28 0.51
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (15 bp):
TTAAAATTTATTTTA
Found at i:2651593 original size:29 final size:29
Alignment explanation
Indices: 2651545--2651602 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2651535 ATATTGATAT
**
2651545 TTAAAATTTATTTTTTTAT-ATTTATTTTA
1 TTAAAATTTATTTTACTATAATTT-TTTTA
2651574 TTAAAATTTATTTTACTATAATTTTTTTA
1 TTAAAATTTATTTTACTATAATTTTTTTA
2651603 GCCAAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TTAAAATTTATTTTACTATAATTTTTTTA
Found at i:2652715 original size:15 final size:15
Alignment explanation
Indices: 2652677--2652726 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2652667 TATATTTTTT
*
2652677 AATTTAATTTTTTAA
1 AATTTAATTTTTAAA
2652692 AA--T-ATTTTTAAA
1 AATTTAATTTTTAAA
**
2652704 AATTTAATTTTTAGT
1 AATTTAATTTTTAAA
2652719 AATTTAAT
1 AATTTAAT
2652727 AATTCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 10 0.34
13 1 0.03
14 1 0.03
15 17 0.59
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:2653165 original size:24 final size:25
Alignment explanation
Indices: 2653138--2653197 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 25
2653128 GTTTTAAAAA
2653138 AATATTAAAATATATTTTTAT-ATT
1 AATATTAAAATATATTTTTATAATT
*
2653162 AATATT--TATATATTTTTATAATT
1 AATATTAAAATATATTTTTATAATT
2653185 AA-ATTAAAATATA
1 AATATTAAAATATA
2653198 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 15 0.48
23 5 0.16
24 11 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTAAAATATATTTTTATAATT
Found at i:2658991 original size:3 final size:3
Alignment explanation
Indices: 2658985--2659028 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2658975 ACTGCTGTTG
2658985 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2659029 TTGTAACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2661630 original size:16 final size:14
Alignment explanation
Indices: 2661601--2661642 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 14
2661591 ACTAAATTAA
*
2661601 AAATATTAAAAAAT
1 AAATATTAATAAAT
2661615 AAATTATATAATAAAT
1 AAA-TAT-TAATAAAT
2661631 AAATATTAATAA
1 AAATATTAATAA
2661643 GGTTATAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
15 6 0.24
16 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTAATAAAT
Found at i:2662393 original size:24 final size:25
Alignment explanation
Indices: 2662334--2662393 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
2662324 TATAATATTT
*
2662334 TATTTTTATTTTTAATATTATCTAAA
1 TATTTTT-TTTTTAATATTATATAAA
* * * *
2662360 TAATTATTTTTTCATATT-TATATA
1 TATTTTTTTTTTAATATTATATAAA
2662384 TATTTTTTTT
1 TATTTTTTTT
2662394 CAAAACTTCC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 12 0.44
25 10 0.37
26 5 0.19
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTTTTTTTAATATTATATAAA
Found at i:2663901 original size:18 final size:18
Alignment explanation
Indices: 2663880--2663932 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2663870 AGGTAGAGAT
*
2663880 AAGGATAGAGAAAAGGAA
1 AAGGAAAGAGAAAAGGAA
* * **
2663898 AAGGAGAGAGACAAGGCT
1 AAGGAAAGAGAAAAGGAA
*
2663916 AAGGAAAGGGAAAAGGA
1 AAGGAAAGAGAAAAGGA
2663933 GAGAGAGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.38, T:0.04
Consensus pattern (18 bp):
AAGGAAAGAGAAAAGGAA
Found at i:2663908 original size:30 final size:30
Alignment explanation
Indices: 2663861--2663938 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
2663851 AGGAGAGGGG
* *
2663861 AAAGGATAAAGG-TAGAGATAAGGAT-AGAGA
1 AAAGGA-AAAGGAGAGAGACAAGGATAAG-GA
*
2663891 AAAGGAAAAGGAGAGAGACAAGGCTAAGGA
1 AAAGGAAAAGGAGAGAGACAAGGATAAGGA
*
2663921 AAGGGAAAAGGAGAGAGA
1 AAAGGAAAAGGAGAGAGA
2663939 GAAACTTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.12
30 35 0.83
31 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.37, T:0.06
Consensus pattern (30 bp):
AAAGGAAAAGGAGAGAGACAAGGATAAGGA
Found at i:2664602 original size:2 final size:2
Alignment explanation
Indices: 2664595--2664632 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2664585 ATAAATGGAT
2664595 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
2664633 ATTATGCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2664797 original size:223 final size:223
Alignment explanation
Indices: 2664409--2664845 Score: 865
Period size: 223 Copynumber: 2.0 Consensus size: 223
2664399 GGAAATTTTA
*
2664409 AATTATGCAGTAATTTTGAACTTCAGTTTTATTTGGAATGAATATGATACACAAGCATTAAAAAT
1 AATTATGCAGTAATTTTGAACTTCAGTTTTATTTGGAATGAATATGATACACAAGCATAAAAAAT
2664474 ATTTAGTGATCAGGCCAAAAGGCTTCTTTAGATGCATGGCTCGGGCTTTGTATCTGATTTTGATA
66 ATTTAGTGATCAGGCCAAAAGGCTTCTTTAGATGCATGGCTCGGGCTTTGTATCTGATTTTGATA
2664539 ACATATTTTGTCTTTGATCTGAGTATATCTTGGTGCATTTGCATTTATAAATGGATTATATATAT
131 ACATATTTTGTCTTTGATCTGAGTATATCTTGGTGCATTTGCATTTATAAATGGATTATATATAT
2664604 ATATATATATATATATATATATATATAT
196 ATATATATATATATATATATATATATAT
2664632 AATTATGCAGTAATTTTGAACTTCAGTTTTATTTGGAATGAATATGATACACAAGCATAAAAAAT
1 AATTATGCAGTAATTTTGAACTTCAGTTTTATTTGGAATGAATATGATACACAAGCATAAAAAAT
2664697 ATTTAGTGATCAGGCCAAAAGGCTTCTTTAGATGCATGGCTCGGGCTTTGTATCTGATTTTGATA
66 ATTTAGTGATCAGGCCAAAAGGCTTCTTTAGATGCATGGCTCGGGCTTTGTATCTGATTTTGATA
2664762 ACATATTTTGTCTTTGATCTGAGTATATCTTGGTGCATTTGCATTTATAAATGGATTATATATAT
131 ACATATTTTGTCTTTGATCTGAGTATATCTTGGTGCATTTGCATTTATAAATGGATTATATATAT
2664827 ATATATATATATATATATA
196 ATATATATATATATATATA
2664846 AGTTGAATTA
Statistics
Matches: 213, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 213 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (223 bp):
AATTATGCAGTAATTTTGAACTTCAGTTTTATTTGGAATGAATATGATACACAAGCATAAAAAAT
ATTTAGTGATCAGGCCAAAAGGCTTCTTTAGATGCATGGCTCGGGCTTTGTATCTGATTTTGATA
ACATATTTTGTCTTTGATCTGAGTATATCTTGGTGCATTTGCATTTATAAATGGATTATATATAT
ATATATATATATATATATATATATATAT
Found at i:2664825 original size:2 final size:2
Alignment explanation
Indices: 2664818--2664845 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2664808 ATAAATGGAT
2664818 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
2664846 AGTTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2673812 original size:3 final size:3
Alignment explanation
Indices: 2673806--2673840 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2673796 TTCTTGTTCC
2673806 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
2673841 CAAAAGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:2674951 original size:22 final size:22
Alignment explanation
Indices: 2674921--2674975 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2674911 ATTTATTTAA
*
2674921 TTTATATTTAAAAATTT-TAAAT
1 TTTAAATTTAAAAATTTAT-AAT
*
2674943 TTTAAATTTAAATATTTATAAT
1 TTTAAATTTAAAAATTTATAAT
2674965 TTTAAAATTTA
1 TTT-AAATTTA
2674976 TATTTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTAAAAATTTATAAT
Found at i:2674968 original size:8 final size:7
Alignment explanation
Indices: 2674932--2674980 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
2674922 TTATATTTAA
2674932 AAATTTT
1 AAATTTT
2674939 AAATTTT
1 AAATTTT
2674946 AAA-TTT
1 AAATTTT
2674952 AAATATTT
1 AAAT-TTT
2674960 ATAATTTT
1 A-AATTTT
*
2674968 AAAATTT
1 AAATTTT
*
2674975 ATATTT
1 AAATTT
2674981 ACATATAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 6 0.17
7 19 0.53
8 8 0.22
9 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AAATTTT
Found at i:2674968 original size:29 final size:30
Alignment explanation
Indices: 2674924--2674986 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2674914 TATTTAATTT
*
2674924 ATATTTAAAAATTTTAAATTTTAAATTTAA
1 ATATTTAAAAATTTTAAAATTTAAATTTAA
* * *
2674954 ATATTT-ATAATTTTAAAATTTATATTTAC
1 ATATTTAAAAATTTTAAAATTTAAATTTAA
2674983 ATAT
1 ATAT
2674987 AAACACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATTTAAAAATTTTAAAATTTAAATTTAA
Found at i:2674975 original size:15 final size:15
Alignment explanation
Indices: 2674933--2674977 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2674923 TATATTTAAA
2674933 AATTTT-AAATTT-T
1 AATTTTAAAATTTAT
*
2674946 AAATTTAAATATTTAT
1 AATTTTAAA-ATTTAT
2674962 AATTTTAAAATTTAT
1 AATTTTAAAATTTAT
2674977 A
1 A
2674978 TTTACATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.19
14 2 0.07
15 11 0.41
16 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTAAAATTTAT
Found at i:2679628 original size:15 final size:15
Alignment explanation
Indices: 2679608--2679658 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2679598 ATTTATATAC
2679608 AATTATAAATTTTAA
1 AATTATAAATTTTAA
2679623 AATTATAAATATTTAA
1 AATTATAAAT-TTTAA
* *
2679639 TA-TAAAAATTTTAA
1 AATTATAAATTTTAA
2679653 ATATTA
1 A-ATTA
2679659 AATAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 5 0.17
15 17 0.57
16 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAAATTTTAA
Found at i:2679647 original size:22 final size:20
Alignment explanation
Indices: 2679621--2679674 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
2679611 TATAAATTTT
2679621 AAAATTATAAATATTTAATATA
1 AAAATTATAAATA-TTAA-ATA
*
2679643 AAAATTTTAAATATTAAATA
1 AAAATTATAAATATTAAATA
*
2679663 AATAAATATAAA
1 AA-AATTATAAA
2679675 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTATAAATATTAAATA
Found at i:2679649 original size:30 final size:27
Alignment explanation
Indices: 2679614--2679695 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 27
2679604 ATACAATTAT
2679614 AAATTTTAAAATTATAAATATTTAATATAA
1 AAATTTTAAAATTATAAATA---AATATAA
2679644 AAATTTTAAATATTAAATAAATAAATATAA
1 AAATTTTAAA-ATT--ATAAATAAATATAA
*
2679674 AAA-ATTAAAA-TATATAATAAAT
1 AAATTTTAAAATTATA-AATAAAT
2679696 TATTATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 1 0.02
28 1 0.02
29 5 0.11
30 20 0.43
31 3 0.06
33 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATTTTAAAATTATAAATAAATATAA
Found at i:2679668 original size:15 final size:15
Alignment explanation
Indices: 2679650--2679717 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
2679640 ATAAAAATTT
2679650 TAAATATTAAATAAA
1 TAAATATTAAATAAA
2679665 TAAATA-TAAA-AAA
1 TAAATATTAAATAAA
2679678 TTAAA-ATATATAATAAA
1 -TAAATAT-TA-AATAAA
* * *
2679695 TTATTATTAATTAAA
1 TAAATATTAAATAAA
*
2679710 TTAATATT
1 TAAATATT
2679718 TTAATTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.09
14 8 0.19
15 20 0.47
16 6 0.14
17 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATATTAAATAAA
Found at i:2679726 original size:18 final size:19
Alignment explanation
Indices: 2679696--2679746 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2679686 TATAATAAAT
2679696 TATTATTAA-TTAAATTA-A
1 TATT-TTAATTTAAATTATA
*
2679714 TATTTTAATTTAATTTATA
1 TATTTTAATTTAAATTATA
*
2679733 TATTTTATTTTAAA
1 TATTTTAATTTAAA
2679747 AATAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 13 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTAATTTAAATTATA
Found at i:2679925 original size:43 final size:43
Alignment explanation
Indices: 2679878--2679967 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
2679868 TTTTATTTAC
2679878 TATTA-ATAAATGTGACTGATAGAGAATCAAAATTATATATTTT
1 TATTAGAT-AATGTGACTGATAGAGAATCAAAATTATATATTTT
* * *
2679921 TATTAGCTAGTGTGGCTGATAGAGAATCAAAATTATATATTTT
1 TATTAGATAATGTGACTGATAGAGAATCAAAATTATATATTTT
2679964 TATT
1 TATT
2679968 TTACTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (43 bp):
TATTAGATAATGTGACTGATAGAGAATCAAAATTATATATTTT
Found at i:2680417 original size:57 final size:57
Alignment explanation
Indices: 2680300--2680418 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
2680290 GCAAATAATC
* * * * * *
2680300 CAATGCTTGGAGTCTATGTATGACCTAGTGTTTCAAATTGCAACCCATCTCTGTCAG
1 CAATGCTTGGAGTCCATGTATGACCTAGGGCTTCAAATTCCAACCCATCCCTATCAG
*
2680357 CAATGCTTGGAGTCCATGTATGACCTAGGGCTTCAAATTCCAACCCATCCCTATCGG
1 CAATGCTTGGAGTCCATGTATGACCTAGGGCTTCAAATTCCAACCCATCCCTATCAG
2680414 CAATG
1 CAATG
2680419 TCTGCATATG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (57 bp):
CAATGCTTGGAGTCCATGTATGACCTAGGGCTTCAAATTCCAACCCATCCCTATCAG
Found at i:2684474 original size:2 final size:2
Alignment explanation
Indices: 2684462--2684520 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
2684452 GTAGTAGTAT
*
2684462 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2684504 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
2684521 TGGACTAGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2686556 original size:2 final size:2
Alignment explanation
Indices: 2686504--2686543 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2686494 TAAATACAAT
2686504 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
2686544 CAATTTCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2686556 original size:15 final size:14
Alignment explanation
Indices: 2686538--2686572 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2686528 TATATATATA
2686538 TATATACAATTTC-
1 TATATACAATTTCT
2686551 TATATACAATTTCT
1 TATATACAATTTCT
*
2686565 TAAATACA
1 TATATACA
2686573 TTCTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATACAATTTCT
Found at i:2686592 original size:2 final size:2
Alignment explanation
Indices: 2686585--2686613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2686575 CTTAAATTTG
2686585 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 A
2686614 ATGGCAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2690417 original size:18 final size:20
Alignment explanation
Indices: 2690394--2690432 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2690384 TGAAATTATG
2690394 AATTTA-AAT-TTATTTAAA
1 AATTTATAATATTATTTAAA
*
2690412 AATTTATATTATTATTTAAA
1 AATTTATAATATTATTTAAA
2690432 A
1 A
2690433 TAATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTATAATATTATTTAAA
Found at i:2690439 original size:12 final size:12
Alignment explanation
Indices: 2690424--2690488 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
2690414 TTTATATTAT
2690424 TATTTAAAATAA
1 TATTTAAAATAA
*
2690436 TATTAAAAAT-A
1 TATTTAAAATAA
* * *
2690447 TTTTTATATTAA
1 TATTTAAAATAA
2690459 TATTTAAAATTAA
1 TATTTAAAA-TAA
*
2690472 -ATTTAAATAAAA
1 TATTTAAA-ATAA
2690484 TATTT
1 TATTT
2690489 TATTTTTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
11 7 0.17
12 25 0.62
13 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:2690894 original size:23 final size:21
Alignment explanation
Indices: 2690863--2690917 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
2690853 TTAGTAAAAT
*
2690863 AAATTTATAATTACTATTATAA
1 AAATATATAATTA-TATTATAA
2690885 AATATATATAATTATATTATAA
1 AA-ATATATAATTATATTATAA
2690907 AAATATA-AATT
1 AAATATATAATT
2690918 TTGTAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 12 0.39
23 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATATAATTATATTATAA
Found at i:2692007 original size:2 final size:2
Alignment explanation
Indices: 2692000--2692024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2691990 AATGTAATTA
2692000 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2692025 ACGGATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2694943 original size:21 final size:19
Alignment explanation
Indices: 2694910--2694950 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2694900 GAACCTCTTA
*
2694910 TTTTAAAATTAAATTAATT
1 TTTTAAAATTAAATCAATT
2694929 TTTTATAAATATAAATCAATT
1 TTTTA-AAAT-TAAATCAATT
2694950 T
1 T
2694951 AATTCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAAAATTAAATCAATT
Found at i:2695060 original size:20 final size:20
Alignment explanation
Indices: 2695021--2695060 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2695011 TTAATATTAA
* * *
2695021 TATATAATTAATATTTAAAT
1 TATATAATAAATAATAAAAT
2695041 TATATAATAAATAATAAAAT
1 TATATAATAAATAATAAAAT
2695061 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAATAAATAATAAAAT
Found at i:2695304 original size:3 final size:3
Alignment explanation
Indices: 2695296--2695328 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2695286 AATTTGAACA
2695296 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2695329 GACGATAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2695553 original size:12 final size:12
Alignment explanation
Indices: 2695536--2695570 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
2695526 CTTGATCGGA
2695536 TAAAAGGAAAAT
1 TAAAAGGAAAAT
2695548 TAAAA-GAAAAT
1 TAAAAGGAAAAT
2695559 TAAAAGTGAAAA
1 TAAAAG-GAAAA
2695571 ATGAAAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (12 bp):
TAAAAGGAAAAT
Found at i:2696482 original size:19 final size:19
Alignment explanation
Indices: 2696454--2696499 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2696444 AATCACTATA
2696454 AAAAAATTATT-TTTATATT
1 AAAAAATTATTATTT-TATT
*
2696473 AAAAATTTATTATTTTATT
1 AAAAAATTATTATTTTATT
2696492 AAATAAAT
1 AAA-AAAT
2696500 AATAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAAAATTATTATTTTATT
Found at i:2699396 original size:19 final size:19
Alignment explanation
Indices: 2699372--2699409 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2699362 GGTAAGTGCC
2699372 GGATATTATCTCATTAATT
1 GGATATTATCTCATTAATT
*
2699391 GGATATTATCTTATTAATT
1 GGATATTATCTCATTAATT
2699410 CTACCCTAAA
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:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (19 bp):
GGATATTATCTCATTAATT
Found at i:2700097 original size:9 final size:9
Alignment explanation
Indices: 2700038--2700096 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
2700028 CACTAACTCA
2700038 AAAAAATTTT
1 AAAAAA-TTT
*
2700048 AAAAAAATCAT
1 -AAAAAAT-TT
*
2700059 AAAAAATTC
1 AAAAAATTT
2700068 AAAAAATTT
1 AAAAAATTT
2700077 --AAAATTT
1 AAAAAATTT
2700084 AAAATAATTT
1 AAAA-AATTT
2700094 AAA
1 AAA
2700097 TTCAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.17
9 10 0.25
10 16 0.40
11 7 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:2700113 original size:15 final size:15
Alignment explanation
Indices: 2700062--2700117 Score: 76
Period size: 16 Copynumber: 3.6 Consensus size: 15
2700052 AAATCATAAA
2700062 AAATTCAAAAAATTT
1 AAATTCAAAAAATTT
*
2700077 AAAATTTAAAATAATTT
1 -AAATTCAAAA-AATTT
2700094 AAATTCAAAAAATTT
1 AAATTCAAAAAATTT
*
2700109 TAATTCAAA
1 AAATTCAAA
2700118 CTCAAATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.36
16 18 0.50
17 5 0.14
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTCAAAAAATTT
Found at i:2700564 original size:4 final size:4
Alignment explanation
Indices: 2700557--2700584 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2700547 TTAAAAAAAA
2700557 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
2700585 GGAGAGTAGG
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:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2701085 original size:32 final size:32
Alignment explanation
Indices: 2700997--2701085 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
2700987 AGGCTCAAAT
* * *
2700997 TAATTTAAAATTTTATTTTATTATATTATTAAA
1 TAATTTAAAATTATATTATATTA-ATAATTAAA
* * *
2701030 T-ATTAAAATATTATTTTATATTAATAATTATA
1 TAATTTAAA-ATTATATTATATTAATAATTAAA
*
2701062 TAATTTAAAATTATATTAAATTAA
1 TAATTTAAAATTATATTATATTAA
2701086 ATTAAAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TAATTTAAAATTATATTATATTAATAATTAAA
Found at i:2705565 original size:16 final size:16
Alignment explanation
Indices: 2705541--2705593 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2705531 CACATGATAA
*
2705541 ATTTTTTTTTTAATTT
1 ATTTATTTTTTAATTT
*
2705557 ATTTATTTTTTATTTTGT
1 ATTTATTTTTTA-ATT-T
* *
2705575 ATATATTTTTTAATGT
1 ATTTATTTTTTAATTT
2705591 ATT
1 ATT
2705594 CGTATCGTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 14 0.48
17 3 0.10
18 12 0.41
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
ATTTATTTTTTAATTT
Found at i:2708527 original size:22 final size:21
Alignment explanation
Indices: 2708486--2708531 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
2708476 TATGTATAAG
2708486 ATTAAACTAAATTTATTTATGA
1 ATTAAACTAAATTTATTTAT-A
2708508 ATTAAGAC-AAATTGTA-TTATA
1 ATTAA-ACTAAATT-TATTTATA
2708529 ATT
1 ATT
2708532 TAAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (21 bp):
ATTAAACTAAATTTATTTATA
Found at i:2708975 original size:3 final size:3
Alignment explanation
Indices: 2708967--2709004 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2708957 ACAGATGCAA
2708967 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2709005 ATTTTGAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2712781 original size:2 final size:2
Alignment explanation
Indices: 2712774--2712804 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2712764 GCTTTCATTT
2712774 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
2712805 GCATGAAAAA
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:2713028 original size:18 final size:18
Alignment explanation
Indices: 2713005--2713057 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
2712995 TAAATTTCTC
2713005 TTTTATATTGTTAATTAA
1 TTTTATATTGTTAATTAA
* *
2713023 TTTTATATATTTTTA-TAA
1 TTTTATAT-TGTTAATTAA
2713041 TTTTATACATTGTTAAT
1 TTTTAT--ATTGTTAAT
2713058 ATTTTAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 17 0.63
19 8 0.30
20 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTATATTGTTAATTAA
Found at i:2713061 original size:18 final size:19
Alignment explanation
Indices: 2713011--2713063 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
2713001 TCTCTTTTAT
*
2713011 ATTGTTAATTAATTTTATAT
1 ATTGTTAA-TAATTTTATAC
*
2713031 ATT-TTTATAATTTTATAC
1 ATTGTTAATAATTTTATAC
2713049 ATTGTTAAT-ATTTTA
1 ATTGTTAATAATTTTA
2713064 ATAAATAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 19 0.66
19 7 0.24
20 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTGTTAATAATTTTATAC
Found at i:2713278 original size:20 final size:20
Alignment explanation
Indices: 2713253--2713291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2713243 ATAAATAATC
*
2713253 TATATAAATAAAATATGATA
1 TATATAAACAAAATATGATA
*
2713273 TATATAAACGAAATATGAT
1 TATATAAACAAAATATGAT
2713292 TGATGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TATATAAACAAAATATGATA
Found at i:2733114 original size:16 final size:16
Alignment explanation
Indices: 2733093--2733127 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2733083 ATTTAAATCC
2733093 CTGACTACAACCCTTA
1 CTGACTACAACCCTTA
2733109 CTGACTACAACCCTTA
1 CTGACTACAACCCTTA
2733125 CTG
1 CTG
2733128 GTAGTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.37, G:0.09, T:0.26
Consensus pattern (16 bp):
CTGACTACAACCCTTA
Found at i:2734422 original size:2 final size:2
Alignment explanation
Indices: 2734415--2734452 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2734405 TTGGCCGGGA
2734415 AG AG AG AG 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 AG AG AG AG
2734453 GACAGTAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2736392 original size:7 final size:7
Alignment explanation
Indices: 2736377--2736410 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
2736367 AATAAATTAT
2736377 AAATATTA
1 AAAT-TTA
2736385 AAATTTA
1 AAATTTA
2736392 AAATTTA
1 AAATTTA
2736399 AAATTTA
1 AAATTTA
2736406 AAATT
1 AAATT
2736411 ATAATATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:2736393 original size:14 final size:13
Alignment explanation
Indices: 2736370--2736411 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
2736360 AATAAAAAAT
2736370 AAATTATAAATATTA
1 AAATT-TAAA-ATTA
2736385 AAATTTAAAATTTA
1 AAATTTAAAA-TTA
2736399 AAATTTAAAATTA
1 AAATTTAAAATTA
2736412 TAATATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.15
14 17 0.65
15 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTTAAAATTA
Found at i:2736994 original size:44 final size:44
Alignment explanation
Indices: 2736944--2737030 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
2736934 ATTAAAATAT
* *
2736944 TTTCGATTTCATTGAATTTTATTCTTAAATTATTGATTTATAAA
1 TTTCGATTTCATTGAATTTAATTCTTAAATTATTAATTTATAAA
2736988 TTTCGATTTCATTGAATTTAATTCTTAAATTATTAATTTATAA
1 TTTCGATTTCATTGAATTTAATTCTTAAATTATTAATTTATAA
2737031 TGTAAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (44 bp):
TTTCGATTTCATTGAATTTAATTCTTAAATTATTAATTTATAAA
Found at i:2737888 original size:26 final size:25
Alignment explanation
Indices: 2737837--2737888 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
2737827 TATTATATTA
*
2737837 AATATAAAATTTTTCTAAAAATAAT
1 AATATAAAATTTTTATAAAAATAAT
*
2737862 AATATAATTATTTTTATATAAAA-AAT
1 AATATAA-AATTTTTATA-AAAATAAT
2737888 A
1 A
2737889 TCATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATAAAATTTTTATAAAAATAAT
Found at i:2737922 original size:16 final size:16
Alignment explanation
Indices: 2737901--2737961 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
2737891 ATATTATAAA
*
2737901 TATTAAAATTTAAATT
1 TATTAAAAATTAAATT
2737917 TATTAAAAATT-AA-T
1 TATTAAAAATTAAATT
2737931 T-TTAAAAA-T-AATT
1 TATTAAAAATTAAATT
*
2737944 ATATAAATAAATTAAATT
1 -TATTAA-AAATTAAATT
2737962 AAACTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 3 0.08
15 5 0.14
16 13 0.35
17 1 0.03
18 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAAAAATTAAATT
Found at i:2738541 original size:20 final size:20
Alignment explanation
Indices: 2738499--2738542 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2738489 GAGGGTGAAA
*
2738499 TTGAATATTTATAATTTTTT
1 TTGAATATTTATAATTTTAT
2738519 TTGAATATTTA-AATTTATAT
1 TTGAATATTTATAATTT-TAT
2738539 TTGA
1 TTGA
2738543 TTTAAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTGAATATTTATAATTTTAT
Found at i:2738598 original size:18 final size:17
Alignment explanation
Indices: 2738560--2738592 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
2738550 AATAATATTT
2738560 ATTAAATA-TTAAATTG
1 ATTAAATATTTAAATTG
2738576 ATTAAATATTATAAATT
1 ATTAAATATT-TAAATT
2738593 ATTTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 1 0.07
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAATATTTAAATTG
Found at i:2742065 original size:17 final size:16
Alignment explanation
Indices: 2742041--2742079 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
2742031 AAATTATTTA
2742041 TTTAATTTTTTAAAAT
1 TTTAATTTTTTAAAAT
2742057 TTATAATTTTTTAAAAT
1 TT-TAATTTTTTAAAAT
2742074 TTTAAT
1 TTTAAT
2742080 ATTATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTTTTTAAAAT
Found at i:2742087 original size:3 final size:3
Alignment explanation
Indices: 2742079--2742119 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2742069 AAAATTTTAA
*
2742079 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2742120 ATTTGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2742431 original size:2 final size:2
Alignment explanation
Indices: 2742424--2742449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2742414 TAAGTTCCAA
2742424 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
2742450 TTTTTGGTTT
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:2742909 original size:30 final size:31
Alignment explanation
Indices: 2742875--2742943 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
2742865 TTTGATTAGG
2742875 TCTAATTAAACCCTTAAAA-ATATATTTTT-T
1 TCTAATTAAACCCTTAAAATAT-TATTTTTGT
* *
2742905 TCTAATTAAGCTCTTAAAATATTATTTTTGT
1 TCTAATTAAACCCTTAAAATATTATTTTTGT
2742936 T-TAATTAA
1 TCTAATTAA
2742944 TCCTTATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (31 bp):
TCTAATTAAACCCTTAAAATATTATTTTTGT
Found at i:2743856 original size:18 final size:19
Alignment explanation
Indices: 2743829--2743865 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2743819 ATTTTAAAAA
2743829 TTAAATAAATTGAACAAAC
1 TTAAATAAATTGAACAAAC
*
2743848 TTAAA-AAATTGATCAAAC
1 TTAAATAAATTGAACAAAC
2743866 CAACTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (19 bp):
TTAAATAAATTGAACAAAC
Found at i:2744637 original size:31 final size:31
Alignment explanation
Indices: 2744599--2744658 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2744589 AAATTGCTCC
2744599 TACCTCTATGGATTGCAAGTAAACTTTATAG
1 TACCTCTATGGATTGCAAGTAAACTTTATAG
* *
2744630 TACCTCTATTGATTGTAAGTAAACTTTAT
1 TACCTCTATGGATTGCAAGTAAACTTTAT
2744659 TCTACAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
TACCTCTATGGATTGCAAGTAAACTTTATAG
Found at i:2747277 original size:22 final size:22
Alignment explanation
Indices: 2747252--2747300 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2747242 TTATTATCTC
2747252 ATTTAAAAAAATATTTAT-ATTT
1 ATTTAAAAAAAT-TTTATAATTT
**
2747274 ATTTTTAAAAATTTTATAATTT
1 ATTTAAAAAAATTTTATAATTT
2747296 ATTTA
1 ATTTA
2747301 TTTATTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTAAAAAAATTTTATAATTT
Found at i:2747283 original size:21 final size:22
Alignment explanation
Indices: 2747258--2747299 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2747248 TCTCATTTAA
2747258 AAAAATATTTAT-ATTTATTTTT
1 AAAAAT-TTTATAATTTATTTTT
2747280 AAAAATTTTATAATTTATTT
1 AAAAATTTTATAATTTATTT
2747300 ATTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAAATTTTATAATTTATTTTT
Found at i:2747843 original size:15 final size:14
Alignment explanation
Indices: 2747814--2747846 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2747804 CAAATATTAA
2747814 TTAA-ATTTAAATT
1 TTAATATTTAAATT
2747827 TTAATATTTATAATT
1 TTAATATTTA-AATT
2747842 TTAAT
1 TTAAT
2747847 TTATTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATATTTAAATT
Found at i:2763649 original size:16 final size:17
Alignment explanation
Indices: 2763628--2763660 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2763618 TCGAAATTGA
2763628 ATTAAAAAATTT-AGTT
1 ATTAAAAAATTTGAGTT
*
2763644 ATTAAATAATTTGAGTT
1 ATTAAAAAATTTGAGTT
2763661 TGAGTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
ATTAAAAAATTTGAGTT
Found at i:2765237 original size:2 final size:2
Alignment explanation
Indices: 2765230--2765285 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2765220 GAAGTCAGTA
2765230 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
2765272 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2765286 GTGTGTGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2766788 original size:39 final size:42
Alignment explanation
Indices: 2766707--2766790 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 42
2766697 TATTATTTAG
*
2766707 TAAATATAATTTTAATATATATTTTATTATTTAATATAAATA
1 TAAATATAATTTTAATATATATTTAATTATTTAATATAAATA
* *
2766749 TAAATATAATTTTTA-ATA-ATTTAATT-TTTAATATTAATA
1 TAAATATAATTTTAATATATATTTAATTATTTAATATAAATA
2766788 TAA
1 TAA
2766791 TTTTAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 15 0.38
40 7 0.18
41 3 0.08
42 14 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (42 bp):
TAAATATAATTTTAATATATATTTAATTATTTAATATAAATA
Found at i:2766791 original size:18 final size:18
Alignment explanation
Indices: 2766745--2766798 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 18
2766735 ATTTAATATA
*
2766745 AATATAAATATAATTTTT
1 AATATTAATATAATTTTT
*
2766763 -A-A-TAATTTAATTTTT
1 AATATTAATATAATTTTT
2766778 AATATTAATATAA-TTTT
1 AATATTAATATAATTTTT
2766795 AATA
1 AATA
2766799 AATCTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 11 0.37
16 2 0.07
17 10 0.33
18 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTAATATAATTTTT
Found at i:2766868 original size:70 final size:74
Alignment explanation
Indices: 2766707--2766896 Score: 205
Period size: 70 Copynumber: 2.6 Consensus size: 74
2766697 TATTATTTAG
*
2766707 TAAATATAATTTTAATATATATTTTATTATTTAATATAAATATAAATATAATTTTTAATAATTTA
1 TAAATATAATTTTAATA-ATATTTAATTATTTAATATAAATATAAATATAATTTTTAATAATTTA
*
2766772 ATTTTTAATA
65 ATATTTAATA
* * * * *
2766782 TTAATATAATTTTAATAA-ATCTTAATTA-TT-ATCTAACTGT-AATATAATTTATTTAT-ATTT
1 TAAATATAATTTTAATAATAT-TTAATTATTTAATATAAATATAAATATAATTT-TTAATAATTT
*
2766842 -ATATTTGATA
64 AATATTTAATA
* *
2766852 TAAATATAATTTTAATAAT-TTATAATTATTTATTATATATATAAA
1 TAAATATAATTTTAATAATATT-TAATTATTTAATATAAATATAAA
2766897 CATTTATTTA
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
69 1 0.01
70 32 0.34
71 16 0.17
72 16 0.17
73 6 0.06
74 7 0.07
75 16 0.17
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (74 bp):
TAAATATAATTTTAATAATATTTAATTATTTAATATAAATATAAATATAATTTTTAATAATTTAA
TATTTAATA
Found at i:2766894 original size:19 final size:20
Alignment explanation
Indices: 2766872--2766951 Score: 65
Period size: 23 Copynumber: 3.8 Consensus size: 20
2766862 TTTAATAATT
2766872 TATAA-TTATTTATTATATA
1 TATAATTTATTTATTATATA
* *
2766891 TATAAACATTTATTTATTCTTTATTCT
1 TAT--A-ATTTATTTA-T-TATA-T-A
2766918 TATAA-TTATTTATTATATA
1 TATAATTTATTTATTATATA
2766937 TATAATTTATTTATT
1 TATAATTTATTTATT
2766952 TATTCTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
19 8 0.17
20 10 0.21
21 4 0.08
22 2 0.04
23 14 0.29
24 2 0.04
25 4 0.08
26 1 0.02
27 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TATAATTTATTTATTATATA
Found at i:2767386 original size:8 final size:9
Alignment explanation
Indices: 2767363--2767391 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2767353 TTAAAAAATA
2767363 TTATAATTT
1 TTATAATTT
2767372 TTATAATTT
1 TTATAATTT
2767381 TT-TAATTT
1 TTATAATTT
2767389 TTA
1 TTA
2767392 GACTTTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATAATTT
Found at i:2768022 original size:2 final size:2
Alignment explanation
Indices: 2768015--2768039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2768005 AAGAAATGTT
2768015 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2768040 TGATTAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2769718 original size:32 final size:31
Alignment explanation
Indices: 2769682--2769742 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2769672 GAATTACCAA
*
2769682 GTTATTAACATCTGTTTTAAATTCTTGTTAGG
1 GTTATCAACATCTG-TTTAAATTCTTGTTAGG
* *
2769714 GTTATCAATATTTGTTTAAATTCTTGTTA
1 GTTATCAACATCTGTTTAAATTCTTGTTA
2769743 TTATCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.52
Consensus pattern (31 bp):
GTTATCAACATCTGTTTAAATTCTTGTTAGG
Found at i:2770325 original size:24 final size:22
Alignment explanation
Indices: 2770298--2770359 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
2770288 ATATTCTCAC
2770298 TTTTTTAATATTTAAATATATAT
1 TTTTTTAATATTTAAATA-ATAT
* * *
2770321 TTTTTAAAAAATTTAATTAATAT
1 TTTTT-TAATATTTAAATAATAT
*
2770344 TTATTTAATATATTAA
1 TTTTTTAATAT-TTAA
2770360 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 4 0.13
23 17 0.55
24 10 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTAATATTTAAATAATAT
Found at i:2770351 original size:11 final size:11
Alignment explanation
Indices: 2770331--2770389 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
2770321 TTTTTAAAAA
2770331 ATTTAATTAAT
1 ATTTAATTAAT
*
2770342 ATTTATTTAAT
1 ATTTAATTAAT
2770353 ATATTAATTAA-
1 AT-TTAATTAAT
*
2770364 A-ATAA-TATAT
1 ATTTAATTA-AT
2770374 ATTTTAATTAAT
1 A-TTTAATTAAT
2770386 ATTT
1 ATTT
2770390 TTATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
8 2 0.05
9 4 0.11
10 1 0.03
11 16 0.42
12 13 0.34
13 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTAATTAAT
Found at i:2770380 original size:21 final size:21
Alignment explanation
Indices: 2770351--2770415 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2770341 TATTTATTTA
*
2770351 ATATATTAATTAAAATAATAT
1 ATATTTTAATTAAAATAATAT
* * *
2770372 ATATTTTAATTAATAT-TTTT
1 ATATTTTAATTAAAATAATAT
*
2770392 ATATTTTTAATAAAAATAATAT
1 ATA-TTTTAATTAAAATAATAT
2770414 AT
1 AT
2770416 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 5 0.15
21 25 0.74
22 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTTAATTAAAATAATAT
Found at i:2770414 original size:20 final size:20
Alignment explanation
Indices: 2770356--2770416 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2770346 ATTTAATATA
*
2770356 TTAATTAAAATAATATATATT
1 TTAATAAAAATAATATAT-TT
* * **
2770377 TTAATTAATATTTTTATATTT
1 TTAA-TAAAAATAATATATTT
2770398 TTAATAAAAATAATATATT
1 TTAATAAAAATAATATATT
2770417 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 11 0.37
21 10 0.33
22 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATAAAAATAATATATTT
Found at i:2770416 original size:40 final size:44
Alignment explanation
Indices: 2770332--2770415 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 44
2770322 TTTTAAAAAA
*
2770332 TTTAATTAATATTTATTTAATATATTAATTAAAATAATATATAT
1 TTTAATTAATATTTATTTAATATATTAATAAAAATAATATATAT
*
2770376 TTTAATTAATA-TT-TTT-ATATTTTTAATAAAAATAATATAT
1 TTTAATTAATATTTATTTAATA-TATTAATAAAAATAATATAT
2770416 TAAATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 21 0.57
43 2 0.05
44 11 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (44 bp):
TTTAATTAATATTTATTTAATATATTAATAAAAATAATATATAT
Found at i:2770863 original size:2 final size:2
Alignment explanation
Indices: 2770856--2770896 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2770846 TGGATGTTTT
2770856 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2770897 TGAGGATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2773536 original size:1 final size:1
Alignment explanation
Indices: 2773532--2773556 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2773522 ACCCCCACCA
2773532 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2773557 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2778657 original size:2 final size:2
Alignment explanation
Indices: 2778650--2778682 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2778640 TACAACAGAC
2778650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2778683 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2781162 original size:2 final size:2
Alignment explanation
Indices: 2781155--2781186 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2781145 TCTGAGTAAA
2781155 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
2781187 CCTTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2782317 original size:2 final size:2
Alignment explanation
Indices: 2782310--2782339 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2782300 GTAAATTGTG
*
2782310 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2782340 ATTAGTGTAT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2784643 original size:25 final size:25
Alignment explanation
Indices: 2784609--2784658 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2784599 AATAAATTAA
*
2784609 AAAAATTTATTTTAACTTCAAATTT
1 AAAAATTTATTTTAACTCCAAATTT
2784634 AAAAATTTATTTTAACTCCAAATTT
1 AAAAATTTATTTTAACTCCAAATTT
2784659 TGATGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAATTTATTTTAACTCCAAATTT
Found at i:2786021 original size:2 final size:2
Alignment explanation
Indices: 2785976--2786013 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2785966 TTTATACAGA
2785976 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
2786014 GCATATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2788683 original size:26 final size:26
Alignment explanation
Indices: 2788654--2788756 Score: 68
Period size: 26 Copynumber: 4.0 Consensus size: 26
2788644 CAAAAGCCAC
2788654 TCTTTGTGTTTATAAAAAATGGTGGT
1 TCTTTGTGTTTATAAAAAATGGTGGT
* * * **
2788680 TCTTTTTTTGTTTGTCAAAAATTATGGT
1 TC--TTTGTGTTTATAAAAAATGGTGGT
* * *
2788708 TGTTTTTGTTTGTAAAAAATGGTGG-
1 TCTTTGTGTTTATAAAAAATGGTGGT
* *
2788733 -C-TTGTTGTTTATCAAAATTGGTGG
1 TCTTTG-TGTTTATAAAAAATGGTGG
2788757 CTAATTTTTA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 2 0.03
24 16 0.27
26 22 0.37
28 20 0.33
ACGTcount: A:0.23, C:0.05, G:0.22, T:0.50
Consensus pattern (26 bp):
TCTTTGTGTTTATAAAAAATGGTGGT
Found at i:2788692 original size:28 final size:26
Alignment explanation
Indices: 2788660--2788738 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 26
2788650 CCACTCTTTG
* *
2788660 TGTTTATAAAAAATGGTGGTTCTTTTTT
1 TGTTTGTAAAAAATGGTGG-T-TGTTTT
* **
2788688 TGTTTGTCAAAAATTATGGTTGTTTT
1 TGTTTGTAAAAAATGGTGGTTGTTTT
2788714 TGTTTGTAAAAAATGGTGGCTTGTT
1 TGTTTGTAAAAAATGGTGG-TTGTT
2788739 GTTTATCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 21 0.50
27 6 0.14
28 15 0.36
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (26 bp):
TGTTTGTAAAAAATGGTGGTTGTTTT
Found at i:2788740 original size:24 final size:24
Alignment explanation
Indices: 2788655--2788758 Score: 75
Period size: 24 Copynumber: 4.1 Consensus size: 24
2788645 AAAAGCCACT
*
2788655 CTTTGTGTTTATAAAAAATGGTGG
1 CTTTTTGTTTATAAAAAATGGTGG
* *
2788679 TTCTTTTTTTGTTTGTCAAAAATTATGGTTG
1 --C--TTTTTGTTTAT-AAAAA--ATGGTGG
*
2788710 -TTTTTGTTTGTAAAAAATGGTGG
1 CTTTTTGTTTATAAAAAATGGTGG
* * *
2788733 CTTGTTGTTTATCAAAATTGGTGG
1 CTTTTTGTTTATAAAAAATGGTGG
2788757 CT
1 CT
2788759 AATTTTTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
23 6 0.09
24 21 0.33
25 5 0.08
26 12 0.19
28 9 0.14
29 5 0.08
31 6 0.09
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (24 bp):
CTTTTTGTTTATAAAAAATGGTGG
Found at i:2788766 original size:23 final size:24
Alignment explanation
Indices: 2788713--2788767 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
2788703 ATGGTTGTTT
* * **
2788713 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTATCAAAAATGGTGGCTAA
*
2788737 TTGTTTATCAAAATTGGTGGCTAA
1 TTGTTTATCAAAAATGGTGGCTAA
2788761 TT-TTTAT
1 TTGTTTAT
2788768 TTCAAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.47
Consensus pattern (24 bp):
TTGTTTATCAAAAATGGTGGCTAA
Found at i:2789944 original size:21 final size:21
Alignment explanation
Indices: 2789918--2789964 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2789908 AGCTGCTTCA
2789918 GATGCATATGTTGCAAAGCAT
1 GATGCATATGTTGCAAAGCAT
*
2789939 GATGCATGTGTTGCAAAGCAT
1 GATGCATATGTTGCAAAGCAT
2789960 GATGC
1 GATGC
2789965 TAGTGACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
GATGCATATGTTGCAAAGCAT
Found at i:2795274 original size:14 final size:14
Alignment explanation
Indices: 2795255--2795282 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2795245 GCATCATTTC
2795255 AAAGCTATAAACAT
1 AAAGCTATAAACAT
2795269 AAAGCTATAAACAT
1 AAAGCTATAAACAT
2795283 CAGTTTTATG
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:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAGCTATAAACAT
Found at i:2800687 original size:34 final size:34
Alignment explanation
Indices: 2800641--2800825 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
2800631 GTAAAAACCA
*
2800641 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2800675 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2800709 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2800743 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2800777 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2800810 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2800826 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2804917 original size:19 final size:19
Alignment explanation
Indices: 2804890--2804952 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2804880 TCACGTGTAC
* *
2804890 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2804909 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2804928 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2804947 AGTACC
1 AGTACC
2804953 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2805304 original size:34 final size:34
Alignment explanation
Indices: 2805258--2805444 Score: 261
Period size: 34 Copynumber: 5.5 Consensus size: 34
2805248 GTAAAAACCA
*
2805258 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2805292 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2805326 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2805360 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2805394 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2805427 CCATTTAATCAACAATGG
1 CCATTTAATCAACAATGG
2805445 CTCCACTTGC
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.15
34 113 0.82
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2805400 original size:102 final size:101
Alignment explanation
Indices: 2805258--2805444 Score: 320
Period size: 102 Copynumber: 1.8 Consensus size: 101
2805248 GTAAAAACCA
2805258 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
*
2805323 CACCCATTTAATCAATAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
2805360 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
2805425 CACCATTTAATCAACAATGG
66 CACCATTTAATCAACAATGG
2805445 CTCCACTTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 17 0.21
102 63 0.79
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:2817908 original size:1 final size:1
Alignment explanation
Indices: 2817893--2817959 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
2817883 TGGCAATTGG
* * * * ** * *
2817893 AAAAAGAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2817958 AA
1 AA
2817960 GTGAAGATTT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2817931 original size:16 final size:16
Alignment explanation
Indices: 2817893--2817959 Score: 80
Period size: 16 Copynumber: 4.1 Consensus size: 16
2817883 TGGCAATTGG
*
2817893 AAAAAGAAAAGAAAAAA
1 AAAAACAAAA-AAAAAA
**
2817910 ACAAAACAAAAAAAAGG
1 A-AAAACAAAAAAAAAA
*
2817927 AAAAAGAAAAAAAAAA
1 AAAAACAAAAAAAAAA
2817943 AAAAACAAAAAAAAAA
1 AAAAACAAAAAAAAAA
2817959 A
1 A
2817960 GTGAAGATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 28 0.67
17 6 0.14
18 8 0.19
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAAAAA
Found at i:2817958 original size:34 final size:34
Alignment explanation
Indices: 2817891--2817956 Score: 118
Period size: 32 Copynumber: 2.0 Consensus size: 34
2817881 CATGGCAATT
2817891 GGAAAAAGAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAGAAAAAAACAAAACAAAAAAAA
2817925 GGAAAAAGAAAA-AAAAAAA-AAAACAAAAAAAA
1 GGAAAAAGAAAAGAAAAAAACAAAACAAAAAAAA
2817957 AAAGTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.41
33 7 0.22
34 12 0.38
ACGTcount: A:0.85, C:0.05, G:0.11, T:0.00
Consensus pattern (34 bp):
GGAAAAAGAAAAGAAAAAAACAAAACAAAAAAAA
Found at i:2820457 original size:23 final size:23
Alignment explanation
Indices: 2820427--2820473 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2820417 TTTATAAATT
2820427 AATTTTTCATACATTAATAGTTC
1 AATTTTTCATACATTAATAGTTC
2820450 AATTTTTCATACATTAATAGTTC
1 AATTTTTCATACATTAATAGTTC
2820473 A
1 A
2820474 GATCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTTTTCATACATTAATAGTTC
Found at i:2821141 original size:2 final size:2
Alignment explanation
Indices: 2821134--2821172 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2821124 TGGCTAGAGT
2821134 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2821173 TAATGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2821527 original size:23 final size:22
Alignment explanation
Indices: 2821479--2821531 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
2821469 ATCCTTCAAA
2821479 ATATAT-TAAAAAATAAAAGAT
1 ATATATATAAAAAATAAAAGAT
*
2821500 -T-TATATAAAAAATAAGAGTAT
1 ATATATATAAAAAATAAAAG-AT
2821521 ATATATATAAA
1 ATATATATAAA
2821532 TATATATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 2 0.07
22 1 0.04
23 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (22 bp):
ATATATATAAAAAATAAAAGAT
Found at i:2825737 original size:12 final size:11
Alignment explanation
Indices: 2825710--2825766 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
2825700 TTATATGATA
2825710 TAAAAAATAAT
1 TAAAAAATAAT
2825721 TAAAAAATAAT
1 TAAAAAATAAT
2825732 TAAAAATATAAT
1 TAAAAA-ATAAT
** *
2825744 ATAATTAATATTT
1 -TAAAAAATA-AT
2825757 TAAAAAATAA
1 TAAAAAATAA
2825767 ATATTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.46
12 15 0.41
13 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAAATAAT
Found at i:2825781 original size:31 final size:30
Alignment explanation
Indices: 2825735--2825800 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
2825725 AAATAATTAA
**
2825735 AAATATAATATAATTAATATTTTAAAAAAT
1 AAATATAATATAATTAATAAATTAAAAAAT
*
2825765 AAATATTATTATAATTAATAAATTAAAAAAT
1 AAATA-TAATATAATTAATAAATTAAAAAAT
2825796 AAATA
1 AAATA
2825801 ATGATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATATAATATAATTAATAAATTAAAAAAT
Found at i:2826474 original size:19 final size:20
Alignment explanation
Indices: 2826438--2826475 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2826428 CTAAGAGTCA
2826438 ATTTAAAGATAAAAATAATT
1 ATTTAAAGATAAAAATAATT
*
2826458 ATTTAAA-ATATAAATAAT
1 ATTTAAAGATAAAAATAAT
2826476 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTTAAAGATAAAAATAATT
Found at i:2826769 original size:23 final size:22
Alignment explanation
Indices: 2826743--2826804 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
2826733 GACATATATC
**
2826743 AATAAAAAAATATGTTTAAATTT
1 AATAAAAAAATAT-TTTAAAAGT
2826766 AATAATAATAAATATTTTAAAAGT
1 AATAA-AA-AAATATTTTAAAAGT
2826790 -ATAAAAAAATTATTT
1 AATAAAAAAA-TATTT
2826805 CTATTAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 9 0.26
24 9 0.26
25 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
AATAAAAAAATATTTTAAAAGT
Found at i:2826979 original size:2 final size:2
Alignment explanation
Indices: 2826972--2827003 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2826962 TTTGGTTACC
2826972 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
2827004 TTATCTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2827628 original size:13 final size:13
Alignment explanation
Indices: 2827610--2827638 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2827600 GAGTCTCCAT
2827610 CTTGAAAGCTTAC
1 CTTGAAAGCTTAC
2827623 CTTGAAAGCTTAC
1 CTTGAAAGCTTAC
2827636 CTT
1 CTT
2827639 ATTTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (13 bp):
CTTGAAAGCTTAC
Found at i:2827920 original size:24 final size:24
Alignment explanation
Indices: 2827892--2827937 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2827882 GATAAAAATT
2827892 AGCCACAAATTTTGACAAACAACA
1 AGCCACAAATTTTGACAAACAACA
*
2827916 AGCCACAATTTTTGACAAACAA
1 AGCCACAAATTTTGACAAACAA
2827938 AAAGGAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.09, T:0.20
Consensus pattern (24 bp):
AGCCACAAATTTTGACAAACAACA
Found at i:2827956 original size:27 final size:27
Alignment explanation
Indices: 2827901--2827996 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
2827891 TAGCCACAAA
* *
2827901 TTTTGACAAACAACAA-G--CCACAAT
1 TTTTGACAAACAAAAAGGAACCACCAT
2827925 TTTTGACAAACAAAAAGGAACCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
* * *
2827952 TTTTGACAAATACAAAGTAACCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
* *
2827979 TGTTGACAAACACAAAGG
1 TTTTGACAAACAAAAAGG
2827997 GTGGCTTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.25
25 1 0.02
27 45 0.74
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.21
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGGAACCACCAT
Found at i:2831925 original size:185 final size:185
Alignment explanation
Indices: 2831613--2831973 Score: 695
Period size: 185 Copynumber: 2.0 Consensus size: 185
2831603 TAATGCCAGA
* *
2831613 TCCTCATCTTTGAAAGATTCATCGACGTTCATCAGATCAGTAACCAGTTGATTGAAACTGGTAAT
1 TCCTCATCTTTGAAAGATTCATCAACATTCATCAGATCAGTAACCAGTTGATTGAAACTGGTAAT
2831678 GTTATCATTCATAGTGGTACCTGCAACATAGGTAAAGCGAAACAATCGCTTCTTCATATGGAGTT
66 GTTATCATTCATAGTGGTACCTGCAACATAGGTAAAGCGAAACAATCGCTTCTTCATATGGAGTT
2831743 TATTCTGACTATTCTTTTTCAAGAATTTCTCCTCCAAAGCTATCCACCTGCTGCT
131 TATTCTGACTATTCTTTTTCAAGAATTTCTCCTCCAAAGCTATCCACCTGCTGCT
2831798 TCCTCATCTTTGAAAGATTCATCAACATTCATCAGATCAGTAACCAGTTGATTGAAACTGGTAAT
1 TCCTCATCTTTGAAAGATTCATCAACATTCATCAGATCAGTAACCAGTTGATTGAAACTGGTAAT
2831863 GTTATCATTCATAGTGGTACCTGCAACATAGGTAAAGCGAAACAATCGCTTCTTCATATGGAGTT
66 GTTATCATTCATAGTGGTACCTGCAACATAGGTAAAGCGAAACAATCGCTTCTTCATATGGAGTT
*
2831928 TATTCTGACTATTCTTTTTCAAGAATTTCTCCTCCAAAGCTGTCCA
131 TATTCTGACTATTCTTTTTCAAGAATTTCTCCTCCAAAGCTATCCA
2831974 TAACTTACTT
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 173 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (185 bp):
TCCTCATCTTTGAAAGATTCATCAACATTCATCAGATCAGTAACCAGTTGATTGAAACTGGTAAT
GTTATCATTCATAGTGGTACCTGCAACATAGGTAAAGCGAAACAATCGCTTCTTCATATGGAGTT
TATTCTGACTATTCTTTTTCAAGAATTTCTCCTCCAAAGCTATCCACCTGCTGCT
Found at i:2832176 original size:17 final size:17
Alignment explanation
Indices: 2832154--2832188 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2832144 CTAGAACTTC
2832154 ACTCTGCCACATGCCAA
1 ACTCTGCCACATGCCAA
2832171 ACTCTGCCACATGCCAA
1 ACTCTGCCACATGCCAA
2832188 A
1 A
2832189 ATGGCCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.40, G:0.11, T:0.17
Consensus pattern (17 bp):
ACTCTGCCACATGCCAA
Done.