Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2567
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: 30857
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:432 original size:15 final size:15
Alignment explanation
Indices: 412--441 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
402 TTTATCTTAC
*
412 ATTTGAGTTTGAATT
1 ATTTGAGTTTAAATT
427 ATTTGAGTTTAAATT
1 ATTTGAGTTTAAATT
442 CTTTTGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
ATTTGAGTTTAAATT
Found at i:2194 original size:30 final size:29
Alignment explanation
Indices: 2076--2208 Score: 90
Period size: 31 Copynumber: 4.4 Consensus size: 29
2066 ATATTCAAGG
* * * *
2076 TTTATTTATATATAATTAAAAGTTAAGAA
1 TTTATTTAAATATAACTAAAAATTAAAAA
* *
2105 TTTATTTTAATATAACTCAAAATCTAAAAAA
1 TTTATTTAAATATAACTAAAAAT-T-AAAAA
* * * * *
2136 TTTATTT-GATGACAAATTAACATTAAAAA
1 TTTATTTAAAT-ATAACTAAAAATTAAAAA
2165 TATTATTTAAATATAA-TAAAAATTAAAAAA
1 T-TTATTTAAATATAACTAAAAATT-AAAAA
2195 TTATTATTTAAATA
1 -T-TTATTTAAATA
2209 ATGTGGACAC
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
29 30 0.37
30 18 0.22
31 34 0.41
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTATTTAAATATAACTAAAAATTAAAAA
Found at i:5412 original size:29 final size:29
Alignment explanation
Indices: 5380--5476 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
5370 AAGTTAAGAA
*
5380 TTATTTTAATATAAATAAATATAAAAAAT
1 TTATTTAAATATAAATAAATATAAAAAAT
** *
5409 TTATTTTGATGA-AAATTAAATATTAAAAA-
1 TTATTTAAAT-ATAAA-TAAATATAAAAAAT
*
5438 -TATTTAAATAT-AATAAAAATATAAAAAT
1 TTATTTAAATATAAATAAATATA-AAAAAT
5466 TTATTTAAATA
1 TTATTTAAATA
5477 ATTGACACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 6 0.11
27 8 0.14
28 7 0.12
29 22 0.39
30 13 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
TTATTTAAATATAAATAAATATAAAAAAT
Found at i:5446 original size:17 final size:18
Alignment explanation
Indices: 5424--5459 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5414 TTGATGAAAA
5424 TTAAATAT-TAAAAATAT
1 TTAAATATATAAAAATAT
5441 TTAAATATAATAAAAATAT
1 TTAAATAT-ATAAAAATAT
5460 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATATATAAAAATAT
Found at i:5449 original size:57 final size:58
Alignment explanation
Indices: 5363--5471 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
5353 TTATTTATAT
* * *
5363 AAATTAAAAGTTAAGAATTATTTTAATATAA-ATAAATATAAAAAATTTATTTTGATGA
1 AAATTAAAAGTTAAGAAATATTTAAATATAATAAAAATAT-AAAAATTTATTTTGATGA
5421 AAATTAAATA-TTAA-AAATATTTAAATATAATAAAAATATAAAAATTTATTT
1 AAATTAAA-AGTTAAGAAATATTTAAATATAATAAAAATATAAAAATTTATTT
5472 AAATAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
57 26 0.57
58 19 0.41
59 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (58 bp):
AAATTAAAAGTTAAGAAATATTTAAATATAATAAAAATATAAAAATTTATTTTGATGA
Found at i:11554 original size:17 final size:17
Alignment explanation
Indices: 11529--11565 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11519 GATGACTTAA
*
11529 ATTACTATTTAAAATAT
1 ATTAATATTTAAAATAT
*
11546 ATTAATATTTAAAATTT
1 ATTAATATTTAAAATAT
11563 ATT
1 ATT
11566 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATATTTAAAATAT
Found at i:12625 original size:2 final size:2
Alignment explanation
Indices: 12618--12643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12608 CAAAAATGAC
12618 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
12644 TTGGTTTACA
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:12940 original size:19 final size:18
Alignment explanation
Indices: 12908--12946 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
12898 TATTATTATG
12908 ATATGATAAAATATATAA
1 ATATGATAAAATATATAA
12926 ATATGATATAAATATATAA
1 ATATGATA-AAATATATAA
12945 AT
1 AT
12947 TATCAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
ATATGATAAAATATATAA
Found at i:13742 original size:11 final size:11
Alignment explanation
Indices: 13672--13742 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
13662 ATAAAAATTT
13672 ATATAAATATA
1 ATATAAATATA
* * *
13683 AAATAATTTTA
1 ATATAAATATA
*
13694 ATATAATTATA
1 ATATAAATATA
* * *
13705 GTATAACAAAAA
1 ATATAA-ATATA
*
13717 TATATAAATAAA
1 -ATATAAATATA
13729 ATATAAATATA
1 ATATAAATATA
13740 ATA
1 ATA
13743 ATCCCATGTA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
11 35 0.76
12 6 0.13
13 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (11 bp):
ATATAAATATA
Found at i:21765 original size:27 final size:26
Alignment explanation
Indices: 21735--21793 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
21725 TGTTAAGAAT
* * *
21735 TTTAAAATTATGTTCGTTTTTGGTTTG
1 TTTAAAAATATGTTCATGTTT-GTTTG
*
21762 TTTAAAAATATTTTCATGTTTGTTTG
1 TTTAAAAATATGTTCATGTTTGTTTG
21788 TTTAAA
1 TTTAAA
21794 TTAAATGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (26 bp):
TTTAAAAATATGTTCATGTTTGTTTG
Found at i:22328 original size:20 final size:21
Alignment explanation
Indices: 22305--22350 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
22295 CATTAATTTA
*
22305 AAAATATATATTTT-AATATT
1 AAAATATAAATTTTAAATATT
22325 AAAAT-TAAATTTTAAATATT
1 AAAATATAAATTTTAAATATT
*
22345 ATAATA
1 AAAATA
22351 AAGGTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATATAAATTTTAAATATT
Found at i:23651 original size:16 final size:16
Alignment explanation
Indices: 23606--23663 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
23596 ATATAATTTT
23606 TAAAA-AAAATA-AAA
1 TAAAATAAAATATAAA
23620 TAAAATAAAATATAAA
1 TAAAATAAAATATAAA
*
23636 T-AAATAAATTATTAAA
1 TAAAATAAAATA-TAAA
23652 TTAAAAATAAAA
1 -T-AAAATAAAA
23664 GACATCAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 5 0.14
15 15 0.42
16 8 0.22
17 1 0.03
19 7 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAAATATAAA
Found at i:23663 original size:5 final size:5
Alignment explanation
Indices: 23606--23643 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
23596 ATATAATTTT
23606 TAAAA -AAAA TAAAA TAAAA TAAAA TATAAA T-AAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAA
23644 TTATTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 18 0.60
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:23844 original size:20 final size:17
Alignment explanation
Indices: 23807--23861 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
23797 TTTATATTTA
23807 ATTTTAATATAAATAAT
1 ATTTTAATATAAATAAT
*
23824 ATTTTAATA-ATATAAT
1 ATTTTAATATAAATAAT
** *
23840 A-AATAATA-AAATAAA
1 ATTTTAATATAAATAAT
23855 ATTTTAA
1 ATTTTAA
23862 ATTAATTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 11 0.37
16 10 0.33
17 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTTAATATAAATAAT
Found at i:23849 original size:30 final size:28
Alignment explanation
Indices: 23778--23861 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 28
23768 TATTATTATT
* *
23778 TAATAATAA-AAATAATATTTTTATATT
1 TAATAATAATAAATAATATTTTAATATA
23805 TAATTTTAAT-ATAAATAATATTTTAATAATA
1 TAA---TAATAATAAATAATATTTTAAT-ATA
*
23836 TAATAAATAATAAAATAAAATTTTAA
1 TAAT-AATAAT-AAATAATATTTTAA
23862 ATTAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 3 0.07
28 1 0.02
29 4 0.09
30 20 0.43
31 18 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATAATAATAAATAATATTTTAATATA
Found at i:23873 original size:30 final size:29
Alignment explanation
Indices: 23782--23891 Score: 77
Period size: 29 Copynumber: 3.7 Consensus size: 29
23772 ATTATTTAAT
* * *
23782 AATA-AAAATAATATTTTTATATTTAATTTT
1 AATATAAAATAA-AATTTTA-AATTAATTTA
*
23812 AATAT-AAATAATATTTT-AA-TAATATAATA
1 AATATAAAATAAAATTTTAAATTAAT-T--TA
23841 AATAATAAAATAAAATTTTAAATTAATTTA
1 AAT-ATAAAATAAAATTTTAAATTAATTTA
*
23871 AAT-TTAAATAAAAATTTTAAA
1 AATATAAAAT-AAAATTTTAAA
23892 AATTTTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
26 4 0.06
27 2 0.03
28 5 0.08
29 19 0.29
30 17 0.26
31 11 0.17
32 3 0.05
33 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATATAAAATAAAATTTTAAATTAATTTA
Found at i:24851 original size:23 final size:24
Alignment explanation
Indices: 24827--24879 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
24817 TGTTTACATT
24827 ATATTTATATATTT-T-ATATATT
1 ATATTTATATATTTATAATATATT
*
24849 -TA-TAATAATATTTATAATATATT
1 ATATTTAT-ATATTTATAATATATT
24872 ATATTTAT
1 ATATTTAT
24880 GTTATGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
20 3 0.12
21 8 0.33
22 1 0.04
23 7 0.29
24 2 0.08
25 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTATATATTTATAATATATT
Found at i:24861 original size:12 final size:11
Alignment explanation
Indices: 24833--24871 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
24823 CATTATATTT
24833 ATATATTT-T-
1 ATATATTTATA
24842 ATATATTTATA
1 ATATATTTATA
24853 ATAATATTTATA
1 AT-ATATTTATA
24865 ATATATT
1 ATATATT
24872 ATATTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
10 1 0.04
11 7 0.26
12 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATTTATA
Found at i:25612 original size:13 final size:13
Alignment explanation
Indices: 25585--25619 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
25575 ATATTAATGA
25585 TTAAATTAA-ATT
1 TTAAATTAATATT
*
25597 TTAATTTAATATT
1 TTAAATTAATATT
25610 TTAAATTAAT
1 TTAAATTAAT
25620 TTGGTATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATTAATATT
Found at i:25836 original size:12 final size:14
Alignment explanation
Indices: 25820--25877 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 14
25810 ATTTAATATT
*
25820 TTAAAAAAT-TTAA
1 TTAAAAAATATAAA
25833 -TAAAAAATATAAA
1 TTAAAAAATATAAA
25846 TTAAAAAATAATTTAAA
1 TTAAAAAAT-A--TAAA
*
25863 TAAAAAAAT-TAAA
1 TTAAAAAATATAAA
25876 TT
1 TT
25878 TATTTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 8 0.22
13 8 0.22
14 8 0.22
15 1 0.03
17 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAAATATAAA
Found at i:25849 original size:17 final size:17
Alignment explanation
Indices: 25829--25871 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
25819 TTTAAAAAAT
25829 TTAATAAAA-AATATAAA
1 TTAA-AAAATAATATAAA
*
25846 TTAAAAAATAATTTAAA
1 TTAAAAAATAATATAAA
*
25863 TAAAAAAAT
1 TTAAAAAAT
25872 TAAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAAAATAATATAAA
Found at i:25867 original size:30 final size:28
Alignment explanation
Indices: 25822--25877 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 28
25812 TTAATATTTT
25822 AAAAAATTTAAT-AAAAAATATAAATTAA
1 AAAAAATTTAATAAAAAAAT-TAAATTAA
25850 AAAATAATTTAAATAAAAAAATTAAATT
1 AAAA-AATTT-AATAAAAAAATTAAATT
25878 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 9 0.36
31 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAAATTTAATAAAAAAATTAAATTAA
Found at i:26129 original size:20 final size:19
Alignment explanation
Indices: 26099--26173 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
26089 CGATTTTGAG
*
26099 TTAAGTTTAAATTTTTAATTT
1 TTAA-TTTAAATTATT-ATTT
26120 TTAATTTAAATTATTA-TT
1 TTAATTTAAATTATTATTT
* *
26138 TTATATATAAATTAATATTT
1 TTA-ATTTAAATTATTATTT
26158 TT-ATTTAAATT-TTATT
1 TTAATTTAAATTATTATT
26174 ATAAAAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
17 4 0.09
18 13 0.28
19 12 0.26
20 14 0.30
21 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TTAATTTAAATTATTATTT
Found at i:26148 original size:19 final size:18
Alignment explanation
Indices: 26106--26173 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
26096 GAGTTAAGTT
* *
26106 TAAATTTTTAATTTTTAATT
1 TAAATTATT-ATTTTT-ATA
26126 TAAATTATTATTTTATATA
1 TAAATTATTATTTT-TATA
* *
26145 TAAATTAATATTTTTATT
1 TAAATTATTATTTTTATA
26163 TAAATT-TTATT
1 TAAATTATTATT
26174 ATAAAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.10
18 9 0.21
19 20 0.48
20 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATTATTATTTTTATA
Found at i:26191 original size:36 final size:37
Alignment explanation
Indices: 26116--26217 Score: 88
Period size: 36 Copynumber: 2.8 Consensus size: 37
26106 TAAATTTTTA
* *
26116 ATTTTTAATTTAAATTATTATTTTATATATAAATTAAT
1 ATTTTTAATTTAAATTATTATTTAAAATATAAA-TAAT
26154 ATTTTT-ATTTAAATT-TTATTATAAAAATATAAA-AAT
1 ATTTTTAATTTAAATTATTATT-T-AAAATATAAATAAT
* * *
26190 A--TTAAATTTAAAATTATTTTTTATAATA
1 ATTTTTAATTT-AAATTATTATTTAAAATA
26218 ATTTTTAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
34 2 0.04
35 9 0.17
36 15 0.28
37 14 0.26
38 14 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
ATTTTTAATTTAAATTATTATTTAAAATATAAATAAT
Found at i:26584 original size:17 final size:16
Alignment explanation
Indices: 26555--26590 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
26545 TATTGTCATA
*
26555 TATATTATTTTTTATAT
1 TATATTATATTTTA-AT
26572 TATATTATATTTTAAT
1 TATATTATATTTTAAT
26588 TAT
1 TAT
26591 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTATATTTTAAT
Found at i:26872 original size:2 final size:2
Alignment explanation
Indices: 26865--26890 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26855 TGCAAAATTA
26865 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
26891 TCTTTCTTCT
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:27137 original size:13 final size:13
Alignment explanation
Indices: 27119--27149 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27109 TTTATAAATC
27119 ATAAAATAATATA
1 ATAAAATAATATA
27132 ATAAAATAATATA
1 ATAAAATAATATA
*
27145 CTAAA
1 ATAAA
27150 TTTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAATAATATA
Found at i:27620 original size:21 final size:20
Alignment explanation
Indices: 27571--27621 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27561 ATATGATATA
*
27571 ATTTTAAAAAATAATGTAAAT
1 ATTTT-AAAAATAATATAAAT
* *
27592 ATTATAAAAATAATATCAAT
1 ATTTTAAAAATAATATAAAT
27612 AGTTTTAAAA
1 A-TTTTAAAA
27622 TTTATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (20 bp):
ATTTTAAAAATAATATAAAT
Found at i:28393 original size:6 final size:6
Alignment explanation
Indices: 28384--28441 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
28374 TCATTTTTAC
* *
28384 TTATAA TTATAA TGATAA -TATAA TTATAA TTATAA TGATAA TTATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
28431 TTATAA TTATA
1 TTATAA TTATA
28442 TATATAGCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 4 0.09
6 43 0.91
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TTATAA
Found at i:28410 original size:23 final size:24
Alignment explanation
Indices: 28384--28441 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
28374 TCATTTTTAC
28384 TTATAATTATAATGATAA-TATAA
1 TTATAATTATAATGATAATTATAA
28407 TTATAATTATAATGATAATTATAA
1 TTATAATTATAATGATAATTATAA
28431 TTATAATTATA
1 TTATAATTATA
28442 TATATAGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
TTATAATTATAATGATAATTATAA
Found at i:29297 original size:17 final size:18
Alignment explanation
Indices: 29256--29322 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
29246 AATTCACATC
* * *
29256 ATATAATTTTAATAATTT
1 ATATTATTTTATTATTTT
*
29274 ATTTTATTTT-TTATTTT
1 ATATTATTTTATTATTTT
*
29291 ATATTATTTTAATTTTTTT
1 ATATTATTTT-ATTATTTT
29310 ATATTATATTTAT
1 ATATTAT-TTTAT
29323 ATAATTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 14 0.35
18 8 0.20
19 15 0.38
20 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTATTTTATTATTTT
Found at i:29316 original size:24 final size:22
Alignment explanation
Indices: 29272--29319 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
29262 TTTTAATAAT
*
29272 TTATTTTATTTTTTATTTTATA
1 TTATTTTATTTTTTATATTATA
29294 TTATTTTAATTTTTTTATATTATA
1 TTATTTT-A-TTTTTTATATTATA
29318 TT
1 TT
29320 TATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 1 0.04
24 15 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTATTTTTTATATTATA
Found at i:29327 original size:24 final size:24
Alignment explanation
Indices: 29280--29328 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
29270 ATTTATTTTA
* *
29280 TTTTTTATTTTATATTATTTTAAT
1 TTTTTTATATTATATTATTATAAT
29304 TTTTTTATATTATATT-TATATAAT
1 TTTTTTATATTATATTAT-TATAAT
29328 T
1 T
29329 ATTATTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTTATATTATATTATTATAAT
Found at i:29620 original size:13 final size:13
Alignment explanation
Indices: 29604--29701 Score: 54
Period size: 13 Copynumber: 7.2 Consensus size: 13
29594 TTATAGAAAT
29604 AAATATAATATAA
1 AAATATAATATAA
**
29617 AAATATAATATTT
1 AAATATAATATAA
* *
29630 AAATTTTATATATA
1 AAATATAATATA-A
*
29644 AATTATTAATATATA
1 AAATA-TAATATA-A
*
29659 AAA-ATTTATATAA
1 AAATA-TAATATAA
* * *
29672 ATATATACTATTTA
1 AAATATAATA-TAA
29686 AAATATAATTATAA
1 AAATATAA-TATAA
29700 AA
1 AA
29702 TAAAAATAAT
Statistics
Matches: 62, Mismatches: 18, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
13 26 0.42
14 24 0.39
15 12 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:29655 original size:15 final size:15
Alignment explanation
Indices: 29609--29660 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 15
29599 GAAATAAATA
*
29609 TAATATA-AAAATA-
1 TAATATATAAATTAT
*
29622 TAATATTTAAATT-T
1 TAATATATAAATTAT
29636 T-ATATATAAATTAT
1 TAATATATAAATTAT
29650 TAATATATAAA
1 TAATATATAAA
29661 AATTTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 16 0.50
14 7 0.22
15 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATATATAAATTAT
Found at i:29700 original size:28 final size:29
Alignment explanation
Indices: 29604--29700 Score: 91
Period size: 27 Copynumber: 3.6 Consensus size: 29
29594 TTATAGAAAT
29604 AAATATAATATA-AAA-ATATAATATTT-
1 AAATATAATATATAAATATATAATATTTA
* * *
29630 AAATTTTATATATAAAT-TATTAATATATA
1 AAATATAATATATAAATATA-TAATATTTA
* *
29659 AAA-AT-TTATATAAATATATACTATTTA
1 AAATATAATATATAAATATATAATATTTA
29686 AAATATAAT-TATAAA
1 AAATATAATATATAAA
29701 ATAAAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
26 10 0.18
27 24 0.43
28 18 0.32
29 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATATAATATATAAATATATAATATTTA
Found at i:29903 original size:11 final size:11
Alignment explanation
Indices: 29886--29921 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
29876 TCGATACGAT
29886 ATAAAAATATA
1 ATAAAAATATA
*
29897 ATTAAAATATA
1 ATAAAAATATA
29908 ATAAAAATATA
1 ATAAAAATATA
29919 ATA
1 ATA
29922 TTTAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:29921 original size:16 final size:16
Alignment explanation
Indices: 29902--29951 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
29892 ATATAATTAA
29902 AATATAATAAAAATAT
1 AATATAATAAAAATAT
29918 AATATTTAATAAATAATATT
1 AATA--TAATAAA-AATA-T
29938 AATAT--TAAAAATAT
1 AATATAATAAAAATAT
29952 TTTAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 4 0.13
16 8 0.27
18 8 0.27
19 4 0.13
20 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATAAAAATAT
Done.