Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold832
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: 25145
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Found at i:613 original size:10 final size:10
Alignment explanation
Indices: 589--653 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
579 AATTAATATT
589 ATAAATT-AA
1 ATAAATTAAA
* *
598 TTAAATTTAA
1 ATAAATTAAA
*
608 ATAAATAAAA
1 ATAAATTAAA
618 ATAAATTAAA
1 ATAAATTAAA
*
628 ATGTTAA-TAAA
1 A--TAAATTAAA
639 ATAAAATTAAA
1 AT-AAATTAAA
650 ATAA
1 ATAA
654 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.16
10 23 0.52
11 11 0.25
12 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:615 original size:23 final size:23
Alignment explanation
Indices: 572--648 Score: 57
Period size: 23 Copynumber: 3.1 Consensus size: 23
562 TATAATTTTA
*
572 TAATTAAAATTAATATTATAAAT
1 TAATTAAAATTAATATAATAAAT
*
595 TAATTAAATTTAA-ATAAATAAAAAT
1 TAATTAAAATTAATAT-AAT--AAAT
* *
620 AAATTAAAATGTTAATAAAATAAAAT
1 TAATTAAAA--TTAATATAAT-AAAT
646 TAA
1 TAA
649 AATAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
22 2 0.05
23 14 0.33
25 11 0.26
26 7 0.17
27 7 0.17
28 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
TAATTAAAATTAATATAATAAAT
Found at i:959 original size:18 final size:18
Alignment explanation
Indices: 926--972 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
916 TTTTAACAAA
926 TTACTT-AAAAATATATT
1 TTACTTAAAAAATATATT
943 TT-CTTAAAAAATAATATT
1 TTACTTAAAAAAT-ATATT
961 TTACTTAAAAAA
1 TTACTTAAAAAA
973 CTATTTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.11
17 8 0.30
18 7 0.26
19 9 0.33
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TTACTTAAAAAATATATT
Found at i:978 original size:17 final size:17
Alignment explanation
Indices: 926--971 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
916 TTTTAACAAA
926 TTACTTAAAAATATATT
1 TTACTTAAAAATATATT
943 TT-CTTAAAAAATAATATT
1 TTACTT-AAAAAT-ATATT
961 TTACTTAAAAA
1 TTACTTAAAAA
972 ACTATTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 8 0.31
18 12 0.46
19 3 0.12
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
TTACTTAAAAATATATT
Found at i:1183 original size:43 final size:42
Alignment explanation
Indices: 1118--1205 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 42
1108 TAAAAAATTA
** * *
1118 TTTTTTATTTTTTTTAAATAAATATTATATGAAATTAAATAAT
1 TTTTTTATTTTTTCCAAATAAATA-AACATGAAATTAAATAAT
** *
1161 TTTTTTATTTTTTCCATTTAAATAAACATGTAATTAAATAAT
1 TTTTTTATTTTTTCCAAATAAATAAACATGAAATTAAATAAT
1203 TTT
1 TTT
1206 ATATATGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 18 0.47
43 20 0.53
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (42 bp):
TTTTTTATTTTTTCCAAATAAATAAACATGAAATTAAATAAT
Found at i:1484 original size:16 final size:16
Alignment explanation
Indices: 1459--1516 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1449 TTTTTAAAAA
*
1459 TTATATTTTATATTTTT
1 TTATA-TTTATATTATT
* *
1476 TTATATTTAAATTAAT
1 TTATATTTATATTATT
*
1492 TTATTTTTATATGTATT
1 TTATATTTATAT-TATT
1509 TTATATTT
1 TTATATTT
1517 CACAAGTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:2000 original size:32 final size:32
Alignment explanation
Indices: 1964--2024 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1954 CGAAACCTAT
*
1964 AATAACTTAAATATTAAAA-TATTTGAATTCGA
1 AATAACTTAAAT-TTAAAATTATTTAAATTCGA
*
1996 AATAATTTAAATTTAAAATTATTTAAATT
1 AATAACTTAAATTTAAAATTATTTAAATT
2025 TAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (32 bp):
AATAACTTAAATTTAAAATTATTTAAATTCGA
Found at i:2008 original size:16 final size:15
Alignment explanation
Indices: 1979--2036 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
1969 CTTAAATATT
*
1979 AAAATATTTGAATTC
1 AAAATATTTAAATTC
* *
1994 GAAATAATTTAAATTT
1 AAAAT-ATTTAAATTC
*
2010 AAAATTATTTAAATTT
1 AAAA-TATTTAAATTC
2026 AAAATATTTAA
1 AAAATATTTAA
2037 GTCTACCCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.30
16 25 0.68
17 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (15 bp):
AAAATATTTAAATTC
Found at i:2035 original size:31 final size:32
Alignment explanation
Indices: 1964--2036 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1954 CGAAACCTAT
* * *
1964 AATAACTTAAATATTAAAATATTTGAATTCGA
1 AATAATTTAAATATTAAAATATTTAAATTCAA
*
1996 AATAATTTAAAT-TTAAAATTATTTAAATTTAA
1 AATAATTTAAATATTAAAA-TATTTAAATTCAA
2028 AAT-ATTTAA
1 AATAATTTAA
2037 GTCTACCCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (32 bp):
AATAATTTAAATATTAAAATATTTAAATTCAA
Found at i:8893 original size:10 final size:10
Alignment explanation
Indices: 8866--8896 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
8856 TCAACTTCAA
8866 TATTAATTTT
1 TATTAATTTT
8876 TATCTAATTTT
1 TAT-TAATTTT
8887 TATTAATTTT
1 TATTAATTTT
8897 AAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTAATTTT
Found at i:9980 original size:17 final size:18
Alignment explanation
Indices: 9952--10005 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
9942 ATCTATCTTG
*
9952 TTTATGATTTATATGAT-T
1 TTTATAATTTATAT-ATAT
*
9970 TTTAT-ATTTATGTATAT
1 TTTATAATTTATATATAT
9987 TTTATAATTTATATTATAT
1 TTTATAATTTATA-TATAT
10006 AAAGAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 2 0.06
17 13 0.42
18 11 0.35
19 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTATAATTTATATATAT
Found at i:10033 original size:20 final size:21
Alignment explanation
Indices: 9990--10038 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9980 TGTATATTTT
*
9990 ATAATTTATATTATATAAAGA
1 ATAATATATATTATATAAAGA
10011 ATAATATAT-TTATAGTAAA-A
1 ATAATATATATTATA-TAAAGA
*
10031 ATATTATA
1 ATAATATA
10039 AAATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
ATAATATATATTATATAAAGA
Found at i:10812 original size:26 final size:25
Alignment explanation
Indices: 10772--10821 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
10762 TTTTTATTAA
** *
10772 TTTTAAATTTTTATAACATATTTTAT
1 TTTTAAATTAATATAA-AAATTTTAT
10798 TTTTAAATTAATATAAAAATTTTA
1 TTTTAAATTAATATAAAAATTTTA
10822 AAAATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTAAATTAATATAAAAATTTTAT
Found at i:10820 original size:19 final size:20
Alignment explanation
Indices: 10796--10837 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10786 AACATATTTT
* *
10796 ATTTTTAAATTAATATAAAA
1 ATTTTAAAAATAATATAAAA
*
10816 ATTTTAAAAATATTATAAAA
1 ATTTTAAAAATAATATAAAA
10836 AT
1 AT
10838 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTTAAAAATAATATAAAA
Found at i:10836 original size:11 final size:11
Alignment explanation
Indices: 10809--10840 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10799 TTTAAATTAA
10809 TATAAAAAT-T
1 TATAAAAATAT
10819 T-TAAAAATAT
1 TATAAAAATAT
10829 TATAAAAATAT
1 TATAAAAATAT
10840 T
1 T
10841 TTTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.35
10 3 0.15
11 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:11329 original size:15 final size:15
Alignment explanation
Indices: 11305--11405 Score: 55
Period size: 14 Copynumber: 7.4 Consensus size: 15
11295 AAAAATAAAA
11305 AATA-ATTAAAATAT
1 AATATATTAAAATAT
11319 AATATATT-AAAT-T
1 AATATATTAAAATAT
* *
11332 TATATAATATAAAT-T
1 AATATATTA-AAATAT
*
11347 ATTATATTAAAAT-T
1 AATATATTAAAATAT
*
11361 --TATA--AATATAT
1 AATATATTAAAATAT
11372 AATAT-TT-AAATAT
1 AATATATTAAAATAT
*
11385 AATTATAATAAAA-AT
1 AA-TATATTAAAATAT
11400 AATATA
1 AATATA
11406 AAATATGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
10 4 0.06
11 1 0.01
12 4 0.06
13 17 0.25
14 20 0.29
15 19 0.28
16 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATTAAAATAT
Found at i:11339 original size:29 final size:29
Alignment explanation
Indices: 11313--11370 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
11303 AAAATAATTA
11313 AAATATAATATATT-AAATTTATATAATAT
1 AAAT-TAATATATTAAAATTTATATAATAT
*
11342 AAATTATTATATTAAAATTTATA-AATAT
1 AAATTAATATATTAAAATTTATATAATAT
11370 A
1 A
11371 TAATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATTAATATATTAAAATTTATATAATAT
Found at i:11382 original size:23 final size:23
Alignment explanation
Indices: 11274--11385 Score: 74
Period size: 23 Copynumber: 5.0 Consensus size: 23
11264 ACTTCGTAAT
*
11274 TAAATA-AGTAAT-TTTAAATTTA
1 TAAATATA-TAATATTTAAATATA
* * * *
11296 AAAATAAAAAATAATTAAA-ATA
1 TAAATATATAATATTTAAATATA
*
11318 T-AATATATTAA-ATTTATATAATA
1 TAAATATA-TAATATTTAAAT-ATA
* * *
11341 TAAAT-TATTATATTAAAATTTA
1 TAAATATATAATATTTAAATATA
11363 TAAATATATAATATTTAAATATA
1 TAAATATATAATATTTAAATATA
11386 ATTATAATAA
Statistics
Matches: 66, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
21 10 0.15
22 21 0.32
23 32 0.48
24 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAAATATATAATATTTAAATATA
Found at i:11519 original size:20 final size:22
Alignment explanation
Indices: 11494--11534 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11484 ATATTATATT
*
11494 AATAA-TA-ATATGATGTAAAA
1 AATAATTAGATATGATATAAAA
11514 AATAATTAGATATGATATAAA
1 AATAATTAGATATGATATAAA
11535 TATATACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (22 bp):
AATAATTAGATATGATATAAAA
Found at i:11765 original size:10 final size:9
Alignment explanation
Indices: 11752--11816 Score: 57
Period size: 9 Copynumber: 7.1 Consensus size: 9
11742 AATTATAATG
11752 ATAAAACTAT
1 ATAAAA-TAT
11762 ATAAAATAT
1 ATAAAATAT
11771 A-AATAA-AT
1 ATAA-AATAT
11779 ATAAAATAT
1 ATAAAATAT
11788 ATATATAATAT
1 ATA-A-AATAT
11799 A-AAAATA-
1 ATAAAATAT
11806 ATTAAAATAT
1 A-TAAAATAT
11816 A
1 A
11817 ATATAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
7 1 0.02
8 11 0.23
9 20 0.43
10 9 0.19
11 6 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAAATAT
Found at i:11780 original size:17 final size:18
Alignment explanation
Indices: 11760--11844 Score: 92
Period size: 17 Copynumber: 5.0 Consensus size: 18
11750 TGATAAAACT
11760 ATATAAAATATAAATA-A
1 ATATAAAATATAAATATA
*
11777 ATATAAAATATATATATA
1 ATATAAAATATAAATATA
11795 ATATAAAA-AT-AAT-TA
1 ATATAAAATATAAATATA
* *
11810 AAATATAATATAAA-ATA
1 ATATAAAATATAAATATA
11827 ATAT-AAATATAATATATA
1 ATATAAAATATAA-ATATA
11845 CATAAACTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
15 8 0.14
16 11 0.20
17 25 0.45
18 12 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAATATAAATATA
Found at i:11791 original size:28 final size:29
Alignment explanation
Indices: 11721--11850 Score: 112
Period size: 28 Copynumber: 4.6 Consensus size: 29
11711 TGATATGAAC
* *
11721 ATATAAAAT-TTTATTAAAT-TAAATTATA
1 ATATAAAATATATATAAAATATAAA-TATA
*
11749 ATGATAAAA-CTATATAAAATATAAATA-A
1 AT-ATAAAATATATATAAAATATAAATATA
* *
11777 ATATAAAATATATATATAATATAAAAATA
1 ATATAAAATATATATAAAATATAAATATA
*
11806 AT-TAAAATATAATATAAAATA-ATATA-A
1 ATATAAAATAT-ATATAAAATATAAATATA
* *
11833 ATATAATATATACATAAA
1 ATATAAAATATATATAAA
11851 CTTAAAATCA
Statistics
Matches: 85, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
27 15 0.18
28 38 0.45
29 28 0.33
30 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (29 bp):
ATATAAAATATATATAAAATATAAATATA
Found at i:11800 original size:5 final size:5
Alignment explanation
Indices: 11766--11842 Score: 61
Period size: 5 Copynumber: 15.2 Consensus size: 5
11756 AACTATATAA
* * *
11766 AATAT AA-AT AA-AT -ATAA AATAT ATATAT AATAT AAAAAT AATTAA
1 AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT -AATAT AA-TAT
*
11811 AATAT AATAT AAAAT AATAT AAATAT AATAT A
1 AATAT AATAT AATAT AATAT -AATAT AATAT A
11843 TACATAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
3 1 0.02
4 7 0.12
5 33 0.57
6 17 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:11849 original size:11 final size:11
Alignment explanation
Indices: 11762--11849 Score: 71
Period size: 11 Copynumber: 8.4 Consensus size: 11
11752 ATAAAACTAT
*
11762 ATAAAATATAA
1 ATAATATATAA
11773 ATAA-ATAT-A
1 ATAATATATAA
*
11782 A-AATATATAT
1 ATAATATATAA
*
11792 ATAATATAAAA
1 ATAATATATAA
*
11803 ATAAT-TAAAA
1 ATAATATATAA
11813 TATAATATA-AA
1 -ATAATATATAA
11824 ATAATATA-AA
1 ATAATATATAA
*
11834 TATAATATATAC
1 -ATAATATATAA
11846 ATAA
1 ATAA
11850 ACTTAAAATC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
8 2 0.03
9 6 0.09
10 20 0.30
11 35 0.53
12 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATATAA
Found at i:11858 original size:45 final size:44
Alignment explanation
Indices: 11735--11842 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 44
11725 AAAATTTTAT
*
11735 TAAAT-TAAATTATAATGATAAAACT-ATATAAAATATAAATAAATA
1 TAAATATAAA-TATAAT-ATAAAAATAAT-TAAAATATAAATAAATA
*
11780 TAAAATATATATATAATATAAAAATAATTAAAATATAATATAAA-A
1 T-AAATATAAATATAATATAAAAATAATTAAAATATAA-ATAAATA
11825 T-AATATAAATATAATATA
1 TAAATATAAATATAATATA
11843 TACATAAACT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
43 16 0.29
45 20 0.36
46 17 0.30
47 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (44 bp):
TAAATATAAATATAATATAAAAATAATTAAAATATAAATAAATA
Found at i:12842 original size:25 final size:24
Alignment explanation
Indices: 12789--12862 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 24
12779 TATAATAAAT
* *
12789 AATTAATTTTTAAAATATTA-AAA
1 AATTAATTTTTAAAATTTTATATA
12812 ATATTAATTTTTAAAAATTTTATATA
1 A-ATTAATTTTT-AAAATTTTATATA
**
12838 AATTAAAATTT-AAATTTTATATA
1 AATTAATTTTTAAAATTTTATATA
12861 AA
1 AA
12863 AAACTCTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 15 0.34
24 10 0.23
25 16 0.36
26 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTAATTTTTAAAATTTTATATA
Found at i:12945 original size:24 final size:23
Alignment explanation
Indices: 12909--12953 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
12899 ATATTCAAAT
* *
12909 TATAAAATCATTTGTTTTATATTA
1 TATAAAATAATTT-TTTGATATTA
*
12933 TATAATATAATTTTTTGATAT
1 TATAAAATAATTTTTTGATAT
12954 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TATAAAATAATTTTTTGATATTA
Found at i:16085 original size:14 final size:14
Alignment explanation
Indices: 16048--16096 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
16038 ACGATATATA
16048 ATTATTATTTATAATT
1 ATTATTATTT-T-ATT
*
16064 -TAATTATTTTATT
1 ATTATTATTTTATT
16077 ATTATTATTTTATT
1 ATTATTATTTTATT
*
16091 AATATT
1 ATTATT
16097 TTGATCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 3 0.10
14 18 0.62
15 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATTATTTTATT
Found at i:16092 original size:26 final size:29
Alignment explanation
Indices: 16048--16108 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
16038 ACGATATATA
*
16048 ATTATTATTTATAATTTAATTATTTT-ATT
1 ATTATTATTTATAATTTAA-TATTTTGATC
16077 ATTATTATTT-T-A-TTAATATTTTGATC
1 ATTATTATTTATAATTTAATATTTTGATC
16103 ATTATT
1 ATTATT
16109 TATTACAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.20
26 12 0.40
27 1 0.03
28 1 0.03
29 10 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (29 bp):
ATTATTATTTATAATTTAATATTTTGATC
Found at i:16329 original size:17 final size:18
Alignment explanation
Indices: 16309--16344 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16299 TTTTCTCTAT
16309 AATAT-AATTTTAAAATA
1 AATATAAATTTTAAAATA
16326 AATATAAATTTTAAAATA
1 AATATAAATTTTAAAATA
16344 A
1 A
16345 TAAATAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATAAATTTTAAAATA
Found at i:16558 original size:26 final size:24
Alignment explanation
Indices: 16529--16577 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16519 TTTTTAAATT
*
16529 TTATTAATTTTAAATAATAATTTAAG
1 TTATTAA-ATTAAATAA-AATTTAAG
*
16555 TTATTAAATTAAATTAAATTTAA
1 TTATTAAATTAAATAAAATTTAA
16578 ATTTAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 7 0.33
26 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATTAAATTAAATAAAATTTAAG
Found at i:20896 original size:20 final size:22
Alignment explanation
Indices: 20873--20917 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
20863 TATTTGTTAT
*
20873 ATTTAATA-TTTATTTAAA-AA
1 ATTTAAAATTTTATTTAAATAA
20893 ATTTAAAATTTTATTTAAATAA
1 ATTTAAAATTTTATTTAAATAA
20915 ATT
1 ATT
20918 GATTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAAATTTTATTTAAATAA
Found at i:21696 original size:16 final size:16
Alignment explanation
Indices: 21675--21712 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
21665 TTAATTTAAG
21675 AATTTTACGTGACAAT
1 AATTTTACGTGACAAT
*
21691 AATTTTACGTGATAAT
1 AATTTTACGTGACAAT
21707 AATTTT
1 AATTTT
21713 TAGACAACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (16 bp):
AATTTTACGTGACAAT
Found at i:22914 original size:27 final size:28
Alignment explanation
Indices: 22884--22937 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
22874 GCAATGAGAG
22884 AAGAAAAAAA-TATAAAAAATATTTTTA
1 AAGAAAAAAATTATAAAAAATATTTTTA
22911 AAGAAAAAAATTATAAAAAATATTTTT
1 AAGAAAAAAATTATAAAAAATATTTTT
22938 TTATTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (28 bp):
AAGAAAAAAATTATAAAAAATATTTTTA
Done.