Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 11 of 31
Found at i:2621673 original size:17 final size:17
Alignment explanation
Indices: 2621653--2621715 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2621643 ATATATTAAT
2621653 ATATTAAAATTTTTATA
1 ATATTAAAATTTTTATA
*
2621670 ATATT--AATTATTA-A
1 ATATTAAAATTTTTATA
* *
2621684 TGTGTTAAAATTTTTATA
1 -ATATTAAAATTTTTATA
*
2621702 ATATATAATATTTT
1 ATAT-TAAAATTTT
2621716 AACACTAGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 9
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
17 14 0.41
18 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATTAAAATTTTTATA
Found at i:2621682 original size:32 final size:33
Alignment explanation
Indices: 2621637--2621717 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 33
2621627 ATATAAAATT
*
2621637 ATATAAATATATTAATATATTAAAATTTTTATA
1 ATATTAATATATTAATATATTAAAATTTTTATA
* *
2621670 ATATTAAT-TATTAATGTGTTAAAATTTTTATA
1 ATATTAATATATTAATATATTAAAATTTTTATA
*
2621702 ATATATAATATTTTAA
1 ATAT-TAATATATTAA
2621718 CACTAGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 26 0.62
33 11 0.26
34 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATTAATATATTAATATATTAAAATTTTTATA
Found at i:2628387 original size:9 final size:9
Alignment explanation
Indices: 2628367--2628422 Score: 51
Period size: 9 Copynumber: 5.7 Consensus size: 9
2628357 TATTTACATA
2628367 TTTTTATAAT
1 TTTTTAT-AT
2628377 TTTTTATAT
1 TTTTTATAT
2628386 TTATTTA-AT
1 TT-TTTATAT
2628395 TTAATTAATATAT
1 TT--TT--TATAT
2628408 TTTTTATAT
1 TTTTTATAT
2628417 TTTTTA
1 TTTTTA
2628423 AAAATTATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
9 19 0.46
10 14 0.34
11 2 0.05
12 2 0.05
13 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:2628454 original size:30 final size:32
Alignment explanation
Indices: 2628420--2628487 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2628410 TTTATATTTT
2628420 TTAAAAAT-TAT-ATATATAATTTTAA-ATAAA
1 TTAAAAATATATAAT-TATAATTTTAATATAAA
* *
2628450 TTAAAAATATTTAATTATTATTTTAATATAAA
1 TTAAAAATATATAATTATAATTTTAATATAAA
2628482 TTAAAA
1 TTAAAA
2628488 TTTTTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 8 0.24
31 12 0.36
32 13 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TTAAAAATATATAATTATAATTTTAATATAAA
Found at i:2630330 original size:31 final size:31
Alignment explanation
Indices: 2630286--2630357 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2630276 ATCAAGGTAT
2630286 AATATAAAAAATTTATTAAAATA-AAATATA
1 AATATAAAAAATTTATTAAAATATAAATATA
* *
2630316 AATATATAAAAATTTATTCAAATATAATTAT-
1 AATATA-AAAAATTTATTAAAATATAAATATA
2630347 AATA-AAAAAAT
1 AATATAAAAAAT
2630358 AATATAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 6 0.16
30 7 0.18
31 20 0.53
32 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (31 bp):
AATATAAAAAATTTATTAAAATATAAATATA
Found at i:2633358 original size:22 final size:22
Alignment explanation
Indices: 2633331--2633374 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2633321 AAATATTTAT
2633331 TTTTAT-ATTAATATTTAAATAA
1 TTTTATAATTAA-ATTTAAATAA
2633353 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
2633375 AAATACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:2634373 original size:21 final size:23
Alignment explanation
Indices: 2634330--2634374 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
2634320 TTAACTGTCT
2634330 AGCTGAAGAATCTGTTAAAAAGA
1 AGCTGAAGAATCTGTTAAAAAGA
2634353 AGCTGAA-AAT-T-TTAGAAAAGA
1 AGCTGAAGAATCTGTTA-AAAAGA
2634374 A
1 A
2634375 AGTAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 3 0.14
23 7 0.33
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (23 bp):
AGCTGAAGAATCTGTTAAAAAGA
Found at i:2638835 original size:14 final size:14
Alignment explanation
Indices: 2638811--2638860 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
2638801 TATTATTGAA
2638811 TTTTTTA-AAATAT
1 TTTTTTATAAATAT
2638824 TTTTTTATAAATAAT
1 TTTTTTATAAAT-AT
*
2638839 TTATTT-T-AA-AT
1 TTTTTTATAAATAT
2638850 TTTTTTATAAA
1 TTTTTTATAAA
2638861 ATAAATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 7 0.23
12 1 0.03
13 11 0.35
14 5 0.16
15 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTATAAATAT
Found at i:2638875 original size:24 final size:25
Alignment explanation
Indices: 2638820--2638882 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
2638810 ATTTTTTAAA
*
2638820 ATATTTTTTTAT-AAATAATTTATTTT
1 ATATTTTTTTATAAAATAA--TATTAT
*
2638846 AAATTTTTTTATAAAATAA-ATTAT
1 ATATTTTTTTATAAAATAATATTAT
*
2638870 ATATTTTTATATA
1 ATATTTTTTTATA
2638883 TATATTTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 15 0.47
26 11 0.34
27 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATTTTTTTATAAAATAATATTAT
Found at i:2639884 original size:28 final size:25
Alignment explanation
Indices: 2639823--2639885 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
2639813 AATAGATATG
2639823 ATATA-AATATATAATATTAAAAAAA
1 ATATATAA-ATATAATATTAAAAAAA
* *
2639848 TTATATAAATATGATATTAACATAAAA
1 ATATATAAATATAATATTAA-A-AAAA
2639875 ATATATTAAAT
1 ATATA-TAAAT
2639886 TTTATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 15 0.48
26 3 0.10
27 8 0.26
28 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATATAAATATAATATTAAAAAAA
Found at i:2639892 original size:28 final size:27
Alignment explanation
Indices: 2639843--2639900 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2639833 ATAATATTAA
2639843 AAAAATTATATAAATATGATATTAACAT
1 AAAAATTATATAAATATGATA-TAACAT
* * *
2639871 AAAAA-TATATTAAATTTTATATAATAT
1 AAAAATTATA-TAAATATGATATAACAT
2639898 AAA
1 AAA
2639901 TTATTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAAATTATATAAATATGATATAACAT
Found at i:2639913 original size:32 final size:30
Alignment explanation
Indices: 2639874--2639941 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
2639864 TTAACATAAA
*
2639874 AATATATTAAATTTTATATAATATAA-ATTATT
1 AATATATTAAA-ATTATATAA-ATAATATT-TT
2639906 AATATATTAAAATTATATAAATAATATTTT
1 AATATATTAAAATTATATAAATAATATTTT
2639936 AA-ATAT
1 AATATAT
2639942 GATTATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.12
30 8 0.24
31 11 0.32
32 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AATATATTAAAATTATATAAATAATATTTT
Found at i:2639920 original size:17 final size:17
Alignment explanation
Indices: 2639874--2639921 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2639864 TTAACATAAA
2639874 AATATATT-AAATT-TT
1 AATATATTAAAATTATT
*
2639889 -ATATAATATAAATTATT
1 AATATATTA-AAATTATT
2639906 AATATATTAAAATTAT
1 AATATATTAAAATTAT
2639922 ATAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.22
16 5 0.19
17 9 0.33
18 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATATTAAAATTATT
Found at i:2641985 original size:17 final size:18
Alignment explanation
Indices: 2641946--2641986 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2641936 ACTTTTAATT
2641946 ATTA-TATTTTTAATAAA
1 ATTATTATTTTTAATAAA
2641963 ATTATTATTTTT-ATAAA
1 ATTATTATTTTTAATAAA
*
2641980 TTTATTA
1 ATTATTA
2641987 ATTAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTATTTTTAATAAA
Found at i:2643153 original size:4 final size:4
Alignment explanation
Indices: 2643146--2643180 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
2643136 TAAATCAAAT
2643146 ATAA ATAA ACTAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA A-T-AA ATAA ATAA ATAA ATAA ATAA A
2643181 AATAAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 24 0.83
5 2 0.07
6 3 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:2643169 original size:18 final size:18
Alignment explanation
Indices: 2643135--2643186 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2643125 TTTAATAAAT
*
2643135 ATAAATCAAATATAAATAA
1 ATAAAT-AAAAATAAATAA
*
2643154 ACTAAA-ATAAATAAATAA
1 A-TAAATAAAAATAAATAA
2643172 ATAAATAAAAATAAA
1 ATAAATAAAAATAAA
2643187 AATCTATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 1 0.04
20 4 0.14
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAATAAAAATAAATAA
Found at i:2643175 original size:26 final size:26
Alignment explanation
Indices: 2643130--2643186 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 26
2643120 AATTTTTTAA
2643130 TAAATATAAATCAAATATAAATAAAC
1 TAAATATAAATCAAATATAAATAAAC
2643156 TAAA-ATAAAT--AA-ATAAATAAA-
1 TAAATATAAATCAAATATAAATAAAC
*
2643177 TAAAAATAAA
1 TAAATATAAA
2643187 AATCTATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 2 0.07
25 6 0.20
26 4 0.13
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAATATAAATCAAATATAAATAAAC
Found at i:2648574 original size:15 final size:15
Alignment explanation
Indices: 2648556--2648608 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
2648546 TAACATTAAT
2648556 AATTTATATTATATA
1 AATTTATATTATATA
2648571 AATTTATATTAT-T-
1 AATTTATATTATATA
2648584 --TTTATATTATATA
1 AATTTATATTATATA
2648597 ATATTT-TATTAT
1 A-ATTTATATTAT
2648609 TTTTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 10 0.30
12 1 0.03
14 1 0.03
15 18 0.55
16 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTATATTATATA
Found at i:2648618 original size:31 final size:26
Alignment explanation
Indices: 2648558--2648620 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
2648548 ACATTAATAA
2648558 TTTATATTATATAAATTTATATTATT
1 TTTATATTATATAAATTTATATTATT
2648584 TTTATATTATATAATATTT-TATTATT
1 TTTATATTATATAA-ATTTATATTATT
*
2648610 TTTATTTTATA
1 TTTATATTATA
2648621 ATTATGTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATATTATATAAATTTATATTATT
Found at i:2650549 original size:19 final size:19
Alignment explanation
Indices: 2650520--2650564 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2650510 TTATTAAAAA
2650520 AATTAAAATATTATTTTTAT
1 AATTAAAATA-TATTTTTAT
*
2650540 -ATTAATATATATTTTTAT
1 AATTAAAATATATTTTTAT
2650558 AATTAAA
1 AATTAAA
2650565 TTTATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTAAAATATATTTTTAT
Found at i:2650786 original size:3 final size:3
Alignment explanation
Indices: 2650771--2650814 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
2650761 ATATATTTAT
2650771 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2650815 AGAGATGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2654800 original size:3 final size:3
Alignment explanation
Indices: 2654792--2654826 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2654782 ATTTTTCAGC
2654792 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2654827 CTAGAATTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2655427 original size:24 final size:24
Alignment explanation
Indices: 2655367--2655429 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
2655357 ATACACGTAT
*
2655367 ATATAAAAATAT-ACATGAAATAA
1 ATATAAAAATATAATATGAAATAA
*
2655390 A-AT-AAATTATTAATATGTAAA-AA
1 ATATAAAAATA-TAATATG-AAATAA
2655413 ATATAAAAATATAATAT
1 ATATAAAAATATAATAT
2655430 TTTAAACACA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 5 0.16
22 3 0.09
23 8 0.25
24 11 0.34
25 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
ATATAAAAATATAATATGAAATAA
Found at i:2655891 original size:23 final size:21
Alignment explanation
Indices: 2655842--2655892 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2655832 CTTAACATAT
*
2655842 ATATAAAAAATAAAAAATACA
1 ATATGAAAAATAAAAAATACA
* *
2655863 ACATGAAAAATAATAAAAATACG
1 ATATGAAAAAT-A-AAAAATACA
2655886 ATATGAA
1 ATATGAA
2655893 TACTTAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 14 0.58
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (21 bp):
ATATGAAAAATAAAAAATACA
Found at i:2656098 original size:20 final size:21
Alignment explanation
Indices: 2656073--2656127 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2656063 AATACATAAA
2656073 ATAAAATA-AAT-TATTAATAT
1 ATAAAATATAATAT-TTAATAT
*
2656093 ATAAAAATATAATATTTTATAT
1 AT-AAAATATAATATTTAATAT
*
2656115 ATAAAAAATAATA
1 ATAAAATATAATA
2656128 CATAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.07
21 16 0.53
22 11 0.37
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATATAATATTTAATAT
Found at i:2656101 original size:21 final size:22
Alignment explanation
Indices: 2656086--2656127 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2656076 AAATAAATTA
2656086 TTAATATATAAAAATATAATAT
1 TTAATATATAAAAATATAATAT
*
2656108 TTTATATATAAAAA-ATAATA
1 TTAATATATAAAAATATAATA
2656128 CATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATATATAAAAATATAATAT
Found at i:2656106 original size:26 final size:23
Alignment explanation
Indices: 2656070--2656127 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
2656060 ATAAATACAT
*
2656070 AAAATAAAATAAATTATTAATATATA
1 AAAATATAAT-AATT-TT-ATATATA
2656096 AAAATATAAT-ATTTTATATATA
1 AAAATATAATAATTTTATATATA
2656118 AAAA-ATAATA
1 AAAATATAATA
2656128 CATAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.17
22 11 0.37
23 2 0.07
24 3 0.10
26 9 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATATAATAATTTTATATATA
Found at i:2659654 original size:16 final size:16
Alignment explanation
Indices: 2659617--2659659 Score: 79
Period size: 15 Copynumber: 2.8 Consensus size: 16
2659607 TTGACTTTTC
2659617 TTTCCCTTATCACCGA
1 TTTCCCTTATCACCGA
2659633 -TTCCCTTATCACCGA
1 TTTCCCTTATCACCGA
2659648 TTTCCCTTATCA
1 TTTCCCTTATCA
2659660 TCAAATCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.19, C:0.37, G:0.05, T:0.40
Consensus pattern (16 bp):
TTTCCCTTATCACCGA
Found at i:2662478 original size:25 final size:23
Alignment explanation
Indices: 2662450--2662495 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
2662440 ATTGTGTATA
*
2662450 TATAATGAATAATTTAAAATATATT
1 TATAATAAATAA-TT-AAATATATT
*
2662475 TATATTAAATAATTAAATATA
1 TATAATAAATAATTAAATATA
2662496 AATAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 2 0.11
25 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAATAAATAATTAAATATATT
Found at i:2662497 original size:6 final size:6
Alignment explanation
Indices: 2662488--2662546 Score: 57
Period size: 6 Copynumber: 9.3 Consensus size: 6
2662478 ATTAAATAAT
**
2662488 TAAATA TAAATA -AAATTA TATTTA TTAAATAA TAAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAA-TA TAAATA -TAAAT-A T-AAATA TAAATA TAAATA
2662539 TAAATA TA
1 TAAATA TA
2662547 TTATATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 3 0.07
6 29 0.66
7 7 0.16
8 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:2662499 original size:14 final size:14
Alignment explanation
Indices: 2662480--2662549 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
2662470 ATATTTATAT
2662480 TAAATAATTAAATA
1 TAAATAATTAAATA
*
2662494 TAAATAAAATTATATTTA
1 TAAAT--AATTA-A-ATA
*
2662512 TTAAATAATAAAATA
1 -TAAATAATTAAATA
2662527 TAAAT-A-TAAATA
1 TAAATAATTAAATA
2662539 TAAATATATTA
1 TAAATA-ATTA
2662550 TATTTATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
12 10 0.23
13 1 0.02
14 11 0.25
15 4 0.09
16 6 0.14
17 5 0.11
18 2 0.05
19 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATAATTAAATA
Found at i:2662519 original size:33 final size:35
Alignment explanation
Indices: 2662464--2662537 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 35
2662454 ATGAATAATT
*
2662464 TAAAA-TATATTTATATTAAATAATTAAATATAAA
1 TAAAATTATATTTATATTAAATAATAAAATATAAA
2662498 TAAAATTATA-TT-TATTAAATAATAAAATATAAA
1 TAAAATTATATTTATATTAAATAATAAAATATAAA
2662531 TATAAAT
1 TA-AAAT
2662538 ATAAATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 22 0.59
34 11 0.30
35 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAAATTATATTTATATTAAATAATAAAATATAAA
Found at i:2662531 original size:39 final size:41
Alignment explanation
Indices: 2662488--2662594 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 41
2662478 ATTAAATAAT
2662488 TAAATATAAATAAAATTATATTTATTA-AAT-AATAAAATA
1 TAAATATAAATAAAATTATATTTATTATAATAAATAAAATA
* * *
2662527 TAAATATAAATATAAA-TATATTATATTTATATTAAATAATATC
1 TAAATATAAATA-AAATTATATT-TA-TTATAATAAATAAAATA
* * *
2662570 TAAAAATTATTAAAATTATATTTAT
1 TAAATATAAATAAAATTATATTTAT
2662595 ATTAAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
39 18 0.32
40 5 0.09
41 4 0.07
42 7 0.12
43 22 0.39
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (41 bp):
TAAATATAAATAAAATTATATTTATTATAATAAATAAAATA
Found at i:2664874 original size:17 final size:18
Alignment explanation
Indices: 2664850--2664889 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
2664840 ATTTTTTATT
2664850 ATATTATAT-T-TAATAA
1 ATATTATATATATAATAA
2664866 A-ATTATATATATAATAA
1 ATATTATATATATAATAA
2664883 ATATTAT
1 ATATTAT
2664890 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 7 0.33
18 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATATATATAATAA
Found at i:2664909 original size:25 final size:27
Alignment explanation
Indices: 2664863--2664913 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
2664853 TTATATTTAA
2664863 TAAAATTATATATATAATAAATATTAT
1 TAAAATTATATATATAATAAATATTAT
2664890 TAAAATTA-AT-TATAATAAATATTA
1 TAAAATTATATATATAATAAATATTA
2664914 ATAATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAATTATATATATAATAAATATTAT
Found at i:2664915 original size:16 final size:15
Alignment explanation
Indices: 2664860--2664933 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
2664850 ATATTATATT
2664860 TAATAAAATT-AT-A
1 TAATAAAATTAATAA
* * *
2664873 T-ATATAATAAATAT
1 TAATAAAATTAATAA
* *
2664887 TATTAAAATTAATTA
1 TAATAAAATTAATAA
2664902 TAATAAATATTAATAA
1 TAATAAA-ATTAATAA
2664918 TAAATTAAAATTAATA
1 T-AA-TAAAATTAATA
2664934 TCATATTAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
12 6 0.13
13 3 0.07
14 1 0.02
15 14 0.31
16 8 0.18
17 9 0.20
18 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAAAATTAATAA
Found at i:2664917 original size:13 final size:13
Alignment explanation
Indices: 2664876--2664922 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2664866 AATTATATAT
2664876 ATAATAAATATTA
1 ATAATAAATATTA
* *
2664889 TTAA-AATTAATT-
1 ATAATAAAT-ATTA
2664901 ATAATAAATATTA
1 ATAATAAATATTA
2664914 ATAATAAAT
1 ATAATAAAT
2664923 TAAAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:2664922 original size:27 final size:27
Alignment explanation
Indices: 2664855--2664933 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
2664845 TTATTATATT
2664855 ATATT-TAATAAAATTATATATATAATAA
1 ATATTATAAT-AAATTA-ATATATAATAA
*
2664883 ATATTATTA-AAATTAAT-TATAATAA
1 ATATTATAATAAATTAATATATAATAA
*
2664908 ATATTAATAATAAATTAAAAT-TAATA
1 ATATT-ATAATAAATTAATATATAATA
2664934 TCATATTAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 13 0.30
26 5 0.11
27 18 0.41
28 6 0.14
29 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTATAATAAATTAATATATAATAA
Found at i:2665382 original size:9 final size:9
Alignment explanation
Indices: 2665355--2665499 Score: 67
Period size: 9 Copynumber: 16.4 Consensus size: 9
2665345 ATGATAATTC
2665355 ATATATATAT
1 ATATATAT-T
2665365 ATATATATT
1 ATATATATT
*
2665374 ATATTTATT
1 ATATATATT
2665383 -T-T-TATT
1 ATATATATT
2665389 ATATAAATTATT
1 ATAT--A-TATT
*
2665401 AAATATATT
1 ATATATATT
*
2665410 A-AAATATT
1 ATATATATT
2665418 A-A-ATA-T
1 ATATATATT
*
2665424 AAATATATT
1 ATATATATT
*
2665433 AAATATATT
1 ATATATATT
2665442 ATAT-TAATT
1 ATATAT-ATT
*
2665451 ATATTTATT
1 ATATATATT
*
2665460 A-AAATATT
1 ATATATATT
*
2665468 ATATGTTATT
1 ATAT-ATATT
*
2665478 ATAT-TTTT
1 ATATATATT
*
2665486 ATATTTTATT
1 ATA-TATATT
2665496 ATAT
1 ATAT
2665500 TTTTATATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 31
0.73 0.07 0.21
Matches are distributed among these distances:
6 6 0.05
7 6 0.05
8 26 0.24
9 41 0.37
10 24 0.22
12 7 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:2665427 original size:23 final size:23
Alignment explanation
Indices: 2665398--2665455 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
2665388 TATATAAATT
2665398 ATTAAATATATTAAA-ATATTAA
1 ATTAAATATATTAAATATATTAA
*
2665420 ATATAAATATATTAAATATATTAT
1 AT-TAAATATATTAAATATATTAA
*
2665444 ATTAATTATATT
1 ATTAAATATATT
2665456 TATTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 22 0.69
24 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAAATATATTAAATATATTAA
Found at i:2665458 original size:15 final size:15
Alignment explanation
Indices: 2665397--2665458 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
2665387 TTATATAAAT
*
2665397 TATTAAATATATTAAAA
1 TATTAAATATATT--TA
**
2665414 TATTAAATATAAATA
1 TATTAAATATATTTA
2665429 TATTAAATATA-TTA
1 TATTAAATATATTTA
*
2665443 TATTAATTATATTTA
1 TATTAAATATATTTA
2665458 T
1 T
2665459 TAAAATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
14 12 0.31
15 16 0.41
17 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAAATATATTTA
Found at i:2665459 original size:4 final size:5
Alignment explanation
Indices: 2665427--2665513 Score: 59
Period size: 5 Copynumber: 19.2 Consensus size: 5
2665417 TAAATATAAA
* *
2665427 TATAT TA-AA TATAT TATAT TA-AT TATAT T-TAT TA-A- AATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
2665472 GT-TAT TATAT T-T-T TATAT TTTAT TATAT T-T-T TATAT TTTAT T
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
2665514 CAAATTATCA
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
3 5 0.08
4 18 0.28
5 40 0.62
6 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:2665478 original size:27 final size:27
Alignment explanation
Indices: 2665429--2665518 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
2665419 AATATAAATA
2665429 TATTAAATATATTATATTAATTATATT
1 TATTAAATATATTATATTAATTATATT
*
2665456 TATTAAA-ATATTATATGTTATTATATT
1 TATTAAATATATTATAT-TAATTATATT
* * *
2665483 T-TTATATTTTATTATATT-TTTATATTT
1 TATTA-AATATATTATATTAATTATA-TT
2665510 TATTCAAAT
1 TATT-AAAT
2665519 TATCAAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
26 17 0.33
27 22 0.42
28 12 0.23
29 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTAAATATATTATATTAATTATATT
Found at i:2665479 original size:10 final size:9
Alignment explanation
Indices: 2665438--2665509 Score: 78
Period size: 9 Copynumber: 8.1 Consensus size: 9
2665428 ATATTAAATA
2665438 TATTATATT
1 TATTATATT
*
2665447 AATTATATT
1 TATTATATT
**
2665456 TATTA-AAA
1 TATTATATT
2665464 TATTATATGT
1 TATTATAT-T
2665474 TATTATATT
1 TATTATATT
2665483 T-TTATATTT
1 TATTATA-TT
2665492 TATTATATT
1 TATTATATT
2665501 T-TTATATT
1 TATTATATT
2665509 T
1 T
2665510 TATTCAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
8 19 0.36
9 21 0.40
10 13 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (9 bp):
TATTATATT
Found at i:2665487 original size:8 final size:8
Alignment explanation
Indices: 2665466--2665510 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
2665456 TATTAAAATA
2665466 TTATATGTT
1 TTATAT-TT
2665475 ATTATATTT
1 -TTATATTT
2665484 TTATATTTT
1 TTATA-TTT
2665493 ATTATATTT
1 -TTATATTT
2665502 TTATATTT
1 TTATATTT
2665510 T
1 T
2665511 ATTCAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 14 0.42
9 8 0.24
10 11 0.33
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATATTT
Found at i:2665487 original size:18 final size:18
Alignment explanation
Indices: 2665438--2665513 Score: 91
Period size: 18 Copynumber: 4.2 Consensus size: 18
2665428 ATATTAAATA
2665438 TATTATATTAATTATA-TT
1 TATTATATT-ATTATATTT
* * *
2665456 TATTAAAATATTATATGT
1 TATTATATTATTATATTT
*
2665474 TATTATATTTTTATATTT
1 TATTATATTATTATATTT
*
2665492 TATTATATTTTTATATTT
1 TATTATATTATTATATTT
2665510 TATT
1 TATT
2665514 CAAATTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 6 0.12
18 44 0.88
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTATATTATTATATTT
Found at i:2667227 original size:21 final size:21
Alignment explanation
Indices: 2667203--2667243 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2667193 ACGACTGTGA
* *
2667203 TGAAGTTAATAATCTGAATTT
1 TGAAGTCAATAACCTGAATTT
*
2667224 TGAAGTCAATGACCTGAATT
1 TGAAGTCAATAACCTGAATT
2667244 AGCACGAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (21 bp):
TGAAGTCAATAACCTGAATTT
Found at i:2667570 original size:2 final size:2
Alignment explanation
Indices: 2667563--2667604 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2667553 ATTGTTATTG
2667563 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
2667605 TTGAAGGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2669434 original size:2 final size:2
Alignment explanation
Indices: 2669429--2669453 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2669419 GTGTGTGAGT
2669429 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2669454 TGCATGCACT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2677567 original size:2 final size:2
Alignment explanation
Indices: 2677560--2677585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2677550 TCCAATACAG
2677560 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
2677586 GATTTTTTTA
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:2678040 original size:27 final size:27
Alignment explanation
Indices: 2678010--2678061 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2678000 CTGCTAAGGG
2678010 CAATATTTTAGACCAAAGGGAATTCGT
1 CAATATTTTAGACCAAAGGGAATTCGT
2678037 CAATATTTTAGACCAAAGGGAATTC
1 CAATATTTTAGACCAAAGGGAATTC
2678062 ATCAGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (27 bp):
CAATATTTTAGACCAAAGGGAATTCGT
Found at i:2685076 original size:2 final size:2
Alignment explanation
Indices: 2685069--2685102 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2685059 AGTCCAAATG
2685069 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
2685103 TCTTGCCACT
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:2685832 original size:30 final size:29
Alignment explanation
Indices: 2685792--2685869 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
2685782 ATCAATTTGG
* *
2685792 TTAAAATTAATTTTAATAATTAAAAAATAT
1 TTAAATTTAATTTTAATAAAT-AAAAATAT
* *
2685822 TTAAATTTAATTATAAAAAATAAAAATAT
1 TTAAATTTAATTTTAATAAATAAAAATAT
**
2685851 TAATAAATTTTTTTTTAAT
1 T--TAAATTTAATTTTAAT
2685870 TTTTTATTAC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 9 0.24
30 17 0.45
31 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAATTTAATTTTAATAAATAAAAATAT
Found at i:2685842 original size:23 final size:24
Alignment explanation
Indices: 2685798--2685843 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2685788 TTGGTTAAAA
*
2685798 TTAATTTTAATAATTAAAAAATAT
1 TTAAATTTAATAATTAAAAAATAT
*
2685822 TTAAATTTAATTA-TAAAAAATA
1 TTAAATTTAATAATTAAAAAATA
2685844 AAAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAATTTAATAATTAAAAAATAT
Found at i:2686537 original size:5 final size:5
Alignment explanation
Indices: 2686502--2686662 Score: 63
Period size: 5 Copynumber: 32.8 Consensus size: 5
2686492 CACGAGATTT
*
2686502 TATTA T-TTA TATAA TATTAA TATTA TTTATTA TATTA TAATTA TATTTA
1 TATTA TATTA TATTA TATT-A TATTA --TATTA TATTA T-ATTA TA-TTA
* * * * * * * *
2686551 AAATA TTTTA TATT- TTTTT TAATA -ATTA -ATAA T-TTA AATTA TATT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* ** * *
2686596 TATTT TAAAA TATTTA TATTA TATTA AATTA TATTA TAATTA T-TT- TATTT
1 TATTA TATTA TA-TTA TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA
2686646 TATTA TATT- T-TTA TATT
1 TATTA TATTA TATTA TATT
2686663 TATGTTAAAT
Statistics
Matches: 115, Mismatches: 25, Indels: 32
0.67 0.15 0.19
Matches are distributed among these distances:
3 3 0.03
4 25 0.22
5 60 0.52
6 22 0.19
7 5 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:2686595 original size:31 final size:35
Alignment explanation
Indices: 2686508--2686630 Score: 91
Period size: 35 Copynumber: 3.6 Consensus size: 35
2686498 ATTTTATTAT
* * *
2686508 TTATATAATATTAATATTATTTATTATATTATAATTATA
1 TTATATAATATTAA-ATTATAT-TTATTTTA-AAATA-A
* *
2686547 TT-TAAAATATT---TTATATTT-TTTT-TAATAA
1 TTATATAATATTAAATTATATTTATTTTAAAATAA
*
2686576 TTA-ATAAT-TTAAATTATATTTATTTTAAAATAT
1 TTATATAATATTAAATTATATTTATTTTAAAATAA
*
2686609 TTATATTATATTAAATTATATT
1 TTATATAATATTAAATTATATT
2686631 ATAATTATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
28 2 0.03
29 7 0.10
30 3 0.04
31 8 0.12
32 7 0.10
33 9 0.13
34 9 0.13
35 12 0.18
38 8 0.12
39 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TTATATAATATTAAATTATATTTATTTTAAAATAA
Found at i:2686604 original size:16 final size:16
Alignment explanation
Indices: 2686583--2686655 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 16
2686573 TAATTAATAA
2686583 TTTAAATTATATTTAT
1 TTTAAATTATATTTAT
2686599 TTTAAA--ATATTTAT
1 TTTAAATTATATTTAT
* * *
2686613 ATTATATTA-AATTAT
1 TTTAAATTATATTTAT
*
2686628 ATTATAATTAT-TTTAT
1 TTTA-AATTATATTTAT
2686644 TTT--ATTATATTT
1 TTTAAATTATATTT
2686656 TTATATTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
13 5 0.11
14 15 0.33
15 9 0.20
16 17 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAATTATATTTAT
Found at i:2686967 original size:2 final size:2
Alignment explanation
Indices: 2686960--2686998 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2686950 ATGCATCCTC
2686960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2686999 GCCACAGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2687484 original size:19 final size:21
Alignment explanation
Indices: 2687457--2687503 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2687447 TATATAAATA
* *
2687457 TTAATATAA-AAATT-ATTTT
1 TTAAAATAATAAATTAAATTT
*
2687476 TTAAAATAATAATTTAAATTT
1 TTAAAATAATAAATTAAATTT
2687497 TTAAAAT
1 TTAAAAT
2687504 TTATAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAATAATAAATTAAATTT
Found at i:2688221 original size:2 final size:2
Alignment explanation
Indices: 2688216--2688249 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2688206 GTAGTGTGTG
* *
2688216 TA TA TA TA TG TA TA TG 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
2688250 AAATTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2693342 original size:18 final size:18
Alignment explanation
Indices: 2693319--2693354 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2693309 TTTAGAGTCA
2693319 ATAATAGATAGATGCATG
1 ATAATAGATAGATGCATG
2693337 ATAATAGATAGATGCATG
1 ATAATAGATAGATGCATG
2693355 CACTGTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
ATAATAGATAGATGCATG
Found at i:2694825 original size:27 final size:27
Alignment explanation
Indices: 2694762--2694825 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
2694752 TTGTTTTTAT
*
2694762 AATAAATATTAAAATAATTTTATAATTA
1 AATAAA-AATAAAATAATTTTATAATTA
** *
2694790 AATTTAAATAAAA-AATTTTATTATTAA
1 AATAAAAATAAAATAATTTTATAATT-A
2694817 AATAAAAAT
1 AATAAAAAT
2694826 TTAAATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 11 0.38
27 14 0.48
28 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATAAAAATAAAATAATTTTATAATTA
Found at i:2695448 original size:22 final size:21
Alignment explanation
Indices: 2695422--2695466 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2695412 TTTTTTTTAC
2695422 ATTTTAAT-TTTAATAAATATAA
1 ATTTTAATGTTT-ATAAAT-TAA
*
2695444 ATTTTTATGTTTATAAATTAA
1 ATTTTAATGTTTATAAATTAA
2695465 AT
1 AT
2695467 AAAAAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 13 0.62
23 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTAATGTTTATAAATTAA
Found at i:2696595 original size:18 final size:18
Alignment explanation
Indices: 2696572--2696615 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2696562 CAATAGGTAA
2696572 AAAAAAAAAAAAAGAAAG
1 AAAAAAAAAAAAAGAAAG
*** *
2696590 AAAAAAGGGAAAGGAAAG
1 AAAAAAAAAAAAAGAAAG
2696608 AAAAAAAA
1 AAAAAAAA
2696616 TTTATATATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAGAAAG
Found at i:2696912 original size:22 final size:23
Alignment explanation
Indices: 2696859--2696913 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
2696849 GTGAAATATG
*
2696859 ATATGAATACAATATAAAAAATA
1 ATATGAATATAATATAAAAAATA
* *
2696882 AT-TAAAATATAGTAT-AAAAATA
1 ATAT-GAATATAATATAAAAAATA
2696904 ATATGAATAT
1 ATATGAATAT
2696914 GATGTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (23 bp):
ATATGAATATAATATAAAAAATA
Found at i:2697547 original size:28 final size:31
Alignment explanation
Indices: 2697483--2697547 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 31
2697473 ATTTATTTTT
2697483 AAATTTAAATAAAAATTTAAATATATAATTA
1 AAATTTAAATAAAAATTTAAATATATAATTA
** * *
2697514 TTATTT-AAT-AAAATTT-ATTTTATAATTA
1 AAATTTAAATAAAAATTTAAATATATAATTA
2697542 AAATTT
1 AAATTT
2697548 TATTAATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 14 0.50
29 7 0.25
30 3 0.11
31 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTTAAATAAAAATTTAAATATATAATTA
Found at i:2697576 original size:21 final size:21
Alignment explanation
Indices: 2697535--2697577 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2697525 AATTTATTTT
* *
2697535 ATAATTAAAATTTTATTAATA
1 ATAACTAAAATTTTATAAATA
2697556 ATAACTAAAATTTCTA-AAATA
1 ATAACTAAAATTT-TATAAATA
2697577 A
1 A
2697578 AATAACGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAACTAAAATTTTATAAATA
Found at i:2697764 original size:5 final size:5
Alignment explanation
Indices: 2697754--2697796 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
2697744 ATATTATTAA
*
2697754 TTTAT TTTAT TTTAT TTATATT TTTAT GTATAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TT-TA-T TTTAT -TTTAT TTTAT TTTAT
2697797 ATATGGGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 22 0.67
6 8 0.24
7 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:2697787 original size:18 final size:17
Alignment explanation
Indices: 2697733--2697794 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
2697723 TATATTTTTG
2697733 TATATTTTTATATATTATT
1 TATATTTTTAT-TA-TATT
* * *
2697752 AATTTATTTTATTTTATT
1 TATAT-TTTTATTATATT
2697770 TATATTTTTATGTATATT
1 TATATTTTTAT-TATATT
2697788 T-TATTTT
1 TATATTTT
2697795 ATATATGGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 12 0.34
18 13 0.37
19 4 0.11
20 6 0.17
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TATATTTTTATTATATT
Found at i:2698305 original size:23 final size:22
Alignment explanation
Indices: 2698266--2698316 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
2698256 CATGTTTGTG
2698266 TTATTTTTTATAT-TTAA-AAT
1 TTATTTTTTATATATTAATAAT
2698286 ATTATATTTTTATATATTAATAAT
1 -TTAT-TTTTTATATATTAATAAT
2698310 TTATTTT
1 TTATTTT
2698317 ATTTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 12 0.44
23 8 0.30
24 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTTTTATATATTAATAAT
Found at i:2699028 original size:21 final size:22
Alignment explanation
Indices: 2699002--2699049 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
2698992 TGTATTTATA
2699002 ATTTTTTATAT-TTAA-AATATT
1 ATTTTTTATATATTAATAAT-TT
2699023 ATTTTTTATATATTAATAATTT
1 ATTTTTTATATATTAATAATTT
2699045 ATTTT
1 ATTTT
2699050 ATTTTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.44
22 11 0.44
23 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTATATATTAATAATTT
Found at i:2699029 original size:23 final size:22
Alignment explanation
Indices: 2699003--2699056 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
2698993 GTATTTATAA
2699003 TTTTTTATATTTAA-AATATTATT
1 TTTTTTATA-TTAATAAT-TTATT
*
2699026 TTTTATATATTAATAATTTATT
1 TTTTTTATATTAATAATTTATT
2699048 TTATTTTAT
1 TT-TTTTAT
2699057 CTATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTTATATTAATAATTTATT
Found at i:2699356 original size:21 final size:21
Alignment explanation
Indices: 2699332--2699385 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
2699322 CGGATATTCA
2699332 TATTATGTTCAT-ATTATTTTT
1 TATTATGTT-ATAATTATTTTT
*
2699353 TATTATGTTTTAATTATTTTT
1 TATTATGTTATAATTATTTTT
2699374 TATTTATGTTAT
1 TA-TTATGTTAT
2699386 GTTCATATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 20 0.69
22 8 0.28
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTATGTTATAATTATTTTT
Found at i:2699358 original size:10 final size:10
Alignment explanation
Indices: 2699343--2699377 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2699333 ATTATGTTCA
2699343 TATTATTTTT
1 TATTATTTTT
2699353 TATTATGTTTT
1 TATTAT-TTTT
*
2699364 AATTATTTTT
1 TATTATTTTT
2699374 TATT
1 TATT
2699378 TATGTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TATTATTTTT
Found at i:2699363 original size:11 final size:11
Alignment explanation
Indices: 2699332--2699383 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
2699322 CGGATATTCA
**
2699332 TATTATGTTCA
1 TATTATGTTTT
2699343 TATTAT-TTTT
1 TATTATGTTTT
2699353 TATTATGTTTT
1 TATTATGTTTT
*
2699364 AATTAT-TTTT
1 TATTATGTTTT
2699374 TATTTATGTT
1 TA-TTATGTT
2699384 ATGTTCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 13 0.38
11 19 0.56
12 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (11 bp):
TATTATGTTTT
Found at i:2700031 original size:28 final size:28
Alignment explanation
Indices: 2699998--2700053 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2699988 CAGATATATT
2699998 TATTTTT-TATATATATTACAATAATTA
1 TATTTTTATATATATATTACAATAATTA
* * *
2700025 TATTTTTATATTTATATTTCAATATTTA
1 TATTTTTATATATATATTACAATAATTA
2700053 T
1 T
2700054 TAAATATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTTTTATATATATATTACAATAATTA
Found at i:2700100 original size:24 final size:26
Alignment explanation
Indices: 2700052--2700104 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
2700042 TTCAATATTT
*
2700052 ATTAAATATGACAATTTTTTTAAAAA
1 ATTAAATATGACAATATTTTTAAAAA
2700078 ATTAAATAT-A-AATATTTTTAAAAA
1 ATTAAATATGACAATATTTTTAAAAA
2700102 ATT
1 ATT
2700105 TTGAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 16 0.62
25 1 0.04
26 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAAATATGACAATATTTTTAAAAA
Found at i:2701637 original size:2 final size:2
Alignment explanation
Indices: 2701630--2701679 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2701620 CATTGCACCG
2701630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2701672 TA TA TA TA
1 TA TA TA TA
2701680 AAAGTAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2702881 original size:2 final size:2
Alignment explanation
Indices: 2702874--2702911 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2702864 TGATCTAGAA
2702874 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
2702912 TTGACGTCCA
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:2703781 original size:21 final size:22
Alignment explanation
Indices: 2703743--2703799 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2703733 TTATTATTTA
*
2703743 AATATATTATAAATTTTTATA-TT
1 AATAT-TTATATA-TTTTATAGTT
2703766 AATATTTATATATTTTATAGTT
1 AATATTTATATATTTTATAGTT
*
2703788 AA-ATTTAAATAT
1 AATATTTATATAT
2703800 AAATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 16 0.52
22 10 0.32
23 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AATATTTATATATTTTATAGTT
Found at i:2705182 original size:40 final size:36
Alignment explanation
Indices: 2705136--2705235 Score: 91
Period size: 37 Copynumber: 2.8 Consensus size: 36
2705126 ATTTAAGATA
2705136 TTATATATATATATATTAATAATTTATTTTATATAAATT
1 TTATATATATATA-ATTAAT-A-TTATTTTATATAAATT
* *
2705175 TTA-ATATATTGATAATTTATATTATTTTATATTAATT
1 TTATATATA-T-ATAATTAATATTATTTTATATAAATT
* *
2705212 TT-TATAT-TATATTTTA-ATTATTTT
1 TTATATATATATAATTAATATTATTTT
2705236 TATGTATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
33 8 0.15
34 7 0.13
35 1 0.02
37 21 0.38
38 6 0.11
39 9 0.16
40 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (36 bp):
TTATATATATATAATTAATATTATTTTATATAAATT
Found at i:2705212 original size:37 final size:33
Alignment explanation
Indices: 2705159--2705235 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 33
2705149 TATTAATAAT
2705159 TTATTTTATATAAATTTTAATATATTGATAATTTATA
1 TTATTTTATATAAATTTT--TATATT-ATAATTTA-A
* *
2705196 TTATTTTATATTAATTTTTATATTATATTTTAA
1 TTATTTTATATAAATTTTTATATTATAATTTAA
2705229 TTATTTT
1 TTATTTT
2705236 TATGTATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 8 0.21
34 7 0.18
35 6 0.16
37 17 0.45
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (33 bp):
TTATTTTATATAAATTTTTATATTATAATTTAA
Found at i:2705216 original size:12 final size:11
Alignment explanation
Indices: 2705190--2705238 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 11
2705180 ATATTGATAA
2705190 TTTATATTA-T
1 TTTATATTATT
2705200 TTTATATTAATT
1 TTTATATT-ATT
2705212 TTTATATTATAT
1 TTTATATTAT-T
2705224 TTTA-ATTATT
1 TTTATATTATT
2705234 TTTAT
1 TTTAT
2705239 GTATGATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 13 0.37
11 8 0.23
12 14 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2705218 original size:22 final size:22
Alignment explanation
Indices: 2705190--2705238 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
2705180 ATATTGATAA
2705190 TTTATA-T-TATTTTATATTAATT
1 TTTATATTATATTTTA-ATT-ATT
2705212 TTTATATTATATTTTAATTATT
1 TTTATATTATATTTTAATTATT
2705234 TTTAT
1 TTTAT
2705239 GTATGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 14 0.56
23 4 0.16
24 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATATTATATTTTAATTATT
Found at i:2705231 original size:11 final size:12
Alignment explanation
Indices: 2705179--2705238 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
2705169 TAAATTTTAA
*
2705179 TATATTGATAATT
1 TATATT-ATATTT
2705192 TATA-T-TATTT
1 TATATTATATTT
2705202 TATATTA-ATTTT
1 TATATTATA-TTT
2705214 TATATTATATTT
1 TATATTATATTT
2705226 TA-ATTAT-TTT
1 TATATTATATTT
2705236 TAT
1 TAT
2705239 GTATGATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
10 13 0.32
11 7 0.17
12 16 0.39
13 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TATATTATATTT
Found at i:2705247 original size:24 final size:24
Alignment explanation
Indices: 2705190--2705247 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
2705180 ATATTGATAA
2705190 TTTATAT--TATTTTATATTAATT
1 TTTATATGATATTTTATATTAATT
*
2705212 TTTATATTATATTTTA-ATT-ATT
1 TTTATATGATATTTTATATTAATT
2705234 TTTATGTATGATAT
1 TTTA--TATGATAT
2705248 AATTACATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 14 0.45
23 3 0.10
24 14 0.45
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTATATGATATTTTATATTAATT
Found at i:2707479 original size:2 final size:2
Alignment explanation
Indices: 2707474--2707515 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2707464 CTTTTTTTTA
2707474 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
2707516 GGTGATTACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2707783 original size:2 final size:2
Alignment explanation
Indices: 2707778--2707803 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2707768 ATAGGGGGGG
2707778 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
2707804 TGGAAAGCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2711504 original size:20 final size:20
Alignment explanation
Indices: 2711460--2711506 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
2711450 TTAAACTTAG
* *
2711460 ATTAAAAATTAGATAACAAT
1 ATTAAAAAATACATAACAAT
*
2711480 A--AAAAAATACATATCAAT
1 ATTAAAAAATACATAACAAT
2711498 ATTAAAAAA
1 ATTAAAAAA
2711507 AGTATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 15 0.68
20 7 0.32
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (20 bp):
ATTAAAAAATACATAACAAT
Found at i:2712159 original size:21 final size:21
Alignment explanation
Indices: 2712106--2712170 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2712096 TACACCTAAG
* *
2712106 ATTATTAAAAATATGTTC-AAA
1 ATTATTAAAATTAT-ATCAAAA
*
2712127 ATTA-TCAAATTATATCAAAA
1 ATTATTAAAATTATATCAAAA
*
2712147 ATTATTAAAATTATATAAAAA
1 ATTATTAAAATTATATCAAAA
2712168 ATT
1 ATT
2712171 TACGGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 21 0.57
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTATTAAAATTATATCAAAA
Found at i:2731089 original size:16 final size:16
Alignment explanation
Indices: 2731070--2731109 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2731060 AGAATTATTA
2731070 AAATTAAAAAACAATC
1 AAATTAAAAAACAATC
** *
2731086 AAATTAAAAATGATTC
1 AAATTAAAAAACAATC
2731102 AAATTAAA
1 AAATTAAA
2731110 CTAATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (16 bp):
AAATTAAAAAACAATC
Found at i:2731136 original size:16 final size:16
Alignment explanation
Indices: 2731084--2731136 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2731074 TAAAAAACAA
*
2731084 TCAAATTAAAAATGAT
1 TCAAATTTAAAATGAT
*
2731100 TCAAATTAAACTAATATGAT
1 TCAAATT----TAAAATGAT
2731120 TCAAATTTAAAATGAT
1 TCAAATTTAAAATGAT
2731136 T
1 T
2731137 TCATCTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 16 0.53
20 14 0.47
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (16 bp):
TCAAATTTAAAATGAT
Found at i:2741888 original size:29 final size:27
Alignment explanation
Indices: 2741855--2741920 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
2741845 ATATTGTTAA
2741855 TTAAATTTAAATAAAAATATTTTTATTAT
1 TTAAATTTAAATAAAAATA-TTTTATT-T
* * *
2741884 TTAAATAATAATTTAAAATATTTTATTT
1 TTAAAT-TTAAATAAAAATATTTTATTT
2741912 TTATAATTT
1 TTA-AATTT
2741921 TATTTAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
28 5 0.16
29 16 0.52
30 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAAATTTAAATAAAAATATTTTATTT
Found at i:2743775 original size:3 final size:3
Alignment explanation
Indices: 2743767--2743791 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2743757 TAATCCCGGT
2743767 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
2743792 TTGTTTCAAG
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:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2748104 original size:2 final size:2
Alignment explanation
Indices: 2748099--2748124 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2748089 TGGGGAAAAA
2748099 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
2748125 GATTTCTGGA
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:2751138 original size:24 final size:23
Alignment explanation
Indices: 2751102--2751146 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2751092 TTGTCATTCA
2751102 AACAATCTTTAAAATAATATGCATG
1 AACAATCTTTAAAA-AA-ATGCATG
2751127 AACAAT-TTTAAAAAAATGCA
1 AACAATCTTTAAAAAAATGCA
2751147 GGTGATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 7 0.35
25 6 0.30
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (23 bp):
AACAATCTTTAAAAAAATGCATG
Found at i:2751868 original size:19 final size:20
Alignment explanation
Indices: 2751838--2751879 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2751828 TAGGAAATGC
2751838 AAAGGTAAAGCCATAAAAAT
1 AAAGGTAAAGCCATAAAAAT
* *
2751858 AAAGG-AAAGCCTTAAAAGT
1 AAAGGTAAAGCCATAAAAAT
2751877 AAA
1 AAA
2751880 CCTTTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAGGTAAAGCCATAAAAAT
Found at i:2759442 original size:2 final size:2
Alignment explanation
Indices: 2759437--2759466 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2759427 ATATCTTGTT
2759437 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
2759467 GGGGGAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2768561 original size:12 final size:12
Alignment explanation
Indices: 2768544--2768568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2768534 CATCCTTTCC
2768544 TCTTCTTCTTTT
1 TCTTCTTCTTTT
2768556 TCTTCTTCTTTT
1 TCTTCTTCTTTT
2768568 T
1 T
2768569 TTCCCCCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCTTCTTTT
Found at i:2768562 original size:15 final size:14
Alignment explanation
Indices: 2768539--2768572 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2768529 GTTTGCATCC
2768539 TTTCCTCTTCTTCTT
1 TTTCCTCTTCTT-TT
*
2768554 TTTCTTCTTCTTTT
1 TTTCCTCTTCTTTT
2768568 TTTCC
1 TTTCC
2768573 CCCACTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCCTCTTCTTTT
Found at i:2769698 original size:17 final size:19
Alignment explanation
Indices: 2769657--2769699 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2769647 TAAACAAAAC
2769657 AACAGACAAGAAAACTCGAAG
1 AACA-ACAAGAAAAC-CGAAG
2769678 AACAACAAGAAAA-CGAA-
1 AACAACAAGAAAACCGAAG
2769695 AACAA
1 AACAA
2769700 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
20 9 0.41
21 4 0.18
ACGTcount: A:0.65, C:0.19, G:0.14, T:0.02
Consensus pattern (19 bp):
AACAACAAGAAAACCGAAG
Found at i:2770223 original size:20 final size:20
Alignment explanation
Indices: 2770198--2770247 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2770188 TTAATTAAAA
*
2770198 ATTTATTAAAAATTATTTAT
1 ATTTATTAAAAATAATTTAT
2770218 ATTTA-TAATAAATAATTTAT
1 ATTTATTAA-AAATAATTTAT
2770238 ATTTATTAAA
1 ATTTATTAAA
2770248 GTTTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTATTAAAAATAATTTAT
Found at i:2770510 original size:20 final size:20
Alignment explanation
Indices: 2770482--2770540 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 20
2770472 TTAAATATCA
2770482 AAATAAATTTTTAATTTAAAT
1 AAAT-AATTTTTAATTTAAAT
2770503 AAATAA--TTTAATTTATAAAT
1 AAATAATTTTTAA-TT-TAAAT
2770523 AAATATATATTTTAATTT
1 AAATA-AT-TTTTAATTT
2770541 TATTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 12 0.38
21 5 0.16
22 1 0.03
23 2 0.06
24 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATTTTTAATTTAAAT
Found at i:2771988 original size:5 final size:5
Alignment explanation
Indices: 2771978--2772016 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
2771968 AATCAACAAC
2771978 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
2772017 AATCAAACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:2772410 original size:2 final size:2
Alignment explanation
Indices: 2772403--2772427 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2772393 GATAAAAATT
2772403 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
2772428 GCCAACTGGA
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:2772732 original size:20 final size:20
Alignment explanation
Indices: 2772689--2772732 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2772679 TTTATACATA
* *
2772689 TAAATAATAATAATATATAT
1 TAAAAAATAATAATATAAAT
2772709 TAAAAAATAATAA-ATAAAT
1 TAAAAAATAATAATATAAAT
2772728 CTAAA
1 -TAAA
2772733 CTTATTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAAATAATAATATAAAT
Found at i:2773802 original size:16 final size:15
Alignment explanation
Indices: 2773780--2773816 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2773770 AATATTGAGA
*
2773780 TTTAAATTTTAAATT
1 TTTAAATATTAAATT
2773795 TATTAAATATTAAATT
1 T-TTAAATATTAAATT
2773811 TTTAAA
1 TTTAAA
2773817 AAGTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATATTAAATT
Found at i:2774056 original size:2 final size:2
Alignment explanation
Indices: 2774049--2774089 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2774039 GACTGTCTCA
2774049 AT AT AT AT 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 AT AT AT AT A
2774090 ACAAGTGCAT
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2774433 original size:2 final size:2
Alignment explanation
Indices: 2774426--2774455 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2774416 TCCGCCACAA
2774426 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
2774456 TGCTTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2774734 original size:16 final size:16
Alignment explanation
Indices: 2774711--2774749 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2774701 TAAAAAAATT
2774711 AATAATTTAAATATAA
1 AATAATTTAAATATAA
* *
2774727 ATTAATTTAAATTTAA
1 AATAATTTAAATATAA
2774743 AATAATT
1 AATAATT
2774750 CAAACTCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAATTTAAATATAA
Found at i:2774841 original size:16 final size:16
Alignment explanation
Indices: 2774805--2774843 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2774795 ATCCAAATCT
*
2774805 GAAATGACTCGAACTC
1 GAAATGACTCAAACTC
* *
2774821 AAAATGACTCAAATTC
1 GAAATGACTCAAACTC
2774837 GAAATGA
1 GAAATGA
2774844 TTTGAATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (16 bp):
GAAATGACTCAAACTC
Found at i:2775893 original size:32 final size:33
Alignment explanation
Indices: 2775851--2775964 Score: 117
Period size: 32 Copynumber: 3.5 Consensus size: 33
2775841 CCGAATCCAT
* * *
2775851 AATGACCCGAACCCGAAGTAACTCAAACTC-AA
1 AATGATCCGAACCCGAAATAACCCAAACTCTAA
* *
2775883 AATGATCCGAACTCGAAATGACCCAAA-TCTAA
1 AATGATCCGAACCCGAAATAACCCAAACTCTAA
* *** *
2775915 AGTGATTTAAACCCGAAATAACCCGAAC-CTAA
1 AATGATCCGAACCCGAAATAACCCAAACTCTAA
2775947 AATGATCCGAACCCGAAA
1 AATGATCCGAACCCGAAA
2775965 ACAACTCGAA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
31 2 0.03
32 62 0.97
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (33 bp):
AATGATCCGAACCCGAAATAACCCAAACTCTAA
Found at i:2776116 original size:10 final size:10
Alignment explanation
Indices: 2776103--2776132 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2776093 CTTATTGATA
2776103 ATGATATATT
1 ATGATATATT
2776113 ATGATATATT
1 ATGATATATT
*
2776123 ATGTTATATT
1 ATGATATATT
2776133 TATTGCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (10 bp):
ATGATATATT
Found at i:2776296 original size:23 final size:22
Alignment explanation
Indices: 2776260--2776304 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2776250 TAAATAAAAG
2776260 TTTTAAATTTAAATA-TTAATA
1 TTTTAAATTTAAATATTTAATA
2776281 TTTTAAAATTTTAAATATTTAATA
1 TTTT-AAA-TTTAAATATTTAATA
2776305 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 3 0.14
23 8 0.38
24 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAATTTAAATATTTAATA
Found at i:2776735 original size:14 final size:14
Alignment explanation
Indices: 2776680--2776735 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
2776670 TTATTCGATA
2776680 TAAATTATTATATAAT
1 TAAA-TATTATAT-AT
2776696 TAAAT-TTATATA-
1 TAAATATTATATAT
*
2776708 -AATATATAATATAT
1 TAA-ATATTATATAT
2776722 TAAATATTATATAT
1 TAAATATTATATAT
2776736 AAAAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
11 2 0.06
12 2 0.06
13 7 0.21
14 16 0.47
15 3 0.09
16 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATATTATATAT
Found at i:2777414 original size:16 final size:17
Alignment explanation
Indices: 2777393--2777424 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2777383 ATATTTATTA
2777393 TAAATA-ATTATATTTT
1 TAAATATATTATATTTT
2777409 TAAATATATTATATTT
1 TAAATATATTATATTT
2777425 ATATCACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATATATTATATTTT
Found at i:2777613 original size:26 final size:23
Alignment explanation
Indices: 2777584--2777646 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 23
2777574 ATTTATTTTA
2777584 TTATTTAAAAATTATAAAATATTATT
1 TTATTTAAAAATTA-AAAATA-T-TT
* *
2777610 TTATATTAATATTTAAAAATATTT
1 TTAT-TTAAAAATTAAAAATATTT
2777634 TTATTTAATAAAT
1 TTATTTAA-AAAT
2777647 AATTATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 4 0.13
24 8 0.26
25 1 0.03
26 10 0.32
27 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAAAAATTAAAAATATTT
Found at i:2777718 original size:28 final size:27
Alignment explanation
Indices: 2777665--2777719 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
2777655 AAATTATATC
* *
2777665 AATTTAAATAATTAAATATTATATTTA
1 AATTTAAATAATCAAATATTAAATTTA
2777692 AATTTAATATAATACAAAT-TTAAATTTA
1 AATTTAA-ATAAT-CAAATATTAAATTTA
2777720 TTAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 13 0.54
29 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTTAAATAATCAAATATTAAATTTA
Found at i:2778032 original size:2 final size:2
Alignment explanation
Indices: 2778025--2778068 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2778015 TATCAATTAC
2778025 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
2778067 AT
1 AT
2778069 TTCCATAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2780098 original size:75 final size:75
Alignment explanation
Indices: 2779998--2780337 Score: 463
Period size: 75 Copynumber: 4.5 Consensus size: 75
2779988 ATTTAGTGCC
* * * *
2779998 ATCTTCAGGCTCCTTCTCTCGCTTTCTCTTCGATGAAGTCTTG-TCAATCTTAACTCC-AGTTTT
1 ATCTTCAGGCTCCTTCTCTCTCTTTCTCTTCAATGAAGT-TTGATAAATCTTAAC-CCTGGTTTT
*
2780061 CTTGGAAGAACT
64 CTTAGAAGAACT
* * * *
2780073 ATCTTCAGGCTCCTTTTCTTTCTTTCTCGTCGATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
1 ATCTTCAGGCTCCTTCTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
2780138 TAGAAGAACT
66 TAGAAGAACT
* * * * *
2780148 ATCTTCAGGTTCCTTATCTCGCTTTCTCTTCAATGAAGTTTGATCAATCTTAACCCCGGTTTTCT
1 ATCTTCAGGCTCCTTCTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
2780213 T-GCAAGAACT
66 TAG-AAGAACT
*
2780223 ATCTTCAGGCTCCTTTTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
1 ATCTTCAGGCTCCTTCTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
*
2780288 CAGAAGAACT
66 TAGAAGAACT
*
2780298 ATCTTCACGCTCCTTCTCTCGT-TTTCTCTTCAATGAAGTT
1 ATCTTCAGGCTCCTTCTCTC-TCTTTCTCTTCAATGAAGTT
2780338 CGATCACTCT
Statistics
Matches: 237, Mismatches: 23, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
74 6 0.03
75 229 0.97
76 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.41
Consensus pattern (75 bp):
ATCTTCAGGCTCCTTCTCTCTCTTTCTCTTCAATGAAGTTTGATAAATCTTAACCCTGGTTTTCT
TAGAAGAACT
Done.